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NO2 over Italy with CAMS European air quality analysis using RELIANCE services

Analysis over a particular country and a town in the country of interest

How to discover RELIANCE datacube resources (spatial & temporal search and subsetting), share resources using EGI datahub, and use RoHub to create FAIR digital Objects

This notebook shows how to discover and access the Copernicus Atmosphere Monitoring products available in the RELIANCE datacube resources, by using the functionalities provided in the Adam API . The process is structured in 7 steps, including example of data analysis and visualization with the Python libraries installed in the Jupyter environment as well as the creation of a FAIR digital object on RoHUB where all the resources used and generated in this notebook are aggregated.

You can customize this Jupyter notebook, for instance by updating the content of Data Management section.

• 1. Data Management

• 2. Authentication

• 3. Datasets Discovery

• 4. Products Discovery

• 5. Data Access

• 6. Data Analysis and Visualizarion

• 7. Create Research Object and Share my work

Step 1: Data Management

Authors

• Make sure you first register to RoHub at https://reliance.rohub.org/.

• We recommend you use your ORCID identifier to login and register to EOSC services.

• In the list of authors, add any co-authors using the email address they used when they registered in RoHub.

author_emails = ['annefou@geo.uio.no', 'jeani@uio.no']

Add the University of Olso and the Nordic e-Infrastructure Collaboration as publishers

UiO_organization = {"org_id":"http://www.uio.no/english/", 
                     "display_name": "University of Oslo", 
                     "agent_type": "organization",
                     "ror_identifier":"01xtthb56",
                     "organization_url": "http://www.uio.no/english/"}

NeIC_organization = {"org_id":"https://neic.no/",
                    "display_name": "Nordic e-Infrastructure Collaboration", 
                     "agent_type": "organization",
                    "ror_identifier":"04jcwf484",
                    "organization_url": "https://neic.no/"}

list_publishers = [UiO_organization, NeIC_organization]

list_copyright_holders = [UiO_organization]

Add the funding

• if your work is not funded set

funded_by = {}

funded_by = {
"grant_id": "101017502",
"grant_Name": "RELIANCE",
"grant_title": "Research Lifecycle Management for Earth Science Communities and Copernicus Users",
"funder_name": "European Commission",
"funder_doi": "10.13039/501100000781",
}

Choose a license for your FAIR digital object

pip install rohub

WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied: rohub in /srv/conda/envs/notebook/lib/python3.9/site-packages (1.0.2)
Requirement already satisfied: pandas in /srv/conda/envs/notebook/lib/python3.9/site-packages (from rohub) (1.3.4)
Requirement already satisfied: requests in /srv/conda/envs/notebook/lib/python3.9/site-packages (from rohub) (2.26.0)
Requirement already satisfied: python-dateutil>=2.7.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (2.7.5)
Requirement already satisfied: pytz>=2017.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (2021.3)
Requirement already satisfied: numpy>=1.17.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (1.20.0)
Requirement already satisfied: six>=1.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas->rohub) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (2021.10.8)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (3.1)
Requirement already satisfied: charset-normalizer~=2.0.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (2.0.0)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (1.26.7)
Note: you may need to restart the kernel to use updated packages.

import rohub

licenses = rohub.list_available_licenses()
# Update line below to print more licenses
licenses[0:5]

['0BSD', 'AAL', 'ADSL', 'AFL-1.1', 'AFL-1.2']

license = 'MIT'

Organize my data using EGI datahub

• Define a prefix for my project (you may need to adjust it for your own usage on your infrastructure).

  • input folder where all the data used as input to my Jupyter Notebook is stored (and eventually shared)

  • output folder where all the results to keep are stored

  • tool folder where all the tools, including this Jupyter Notebook will be copied for sharing

• Create all corresponding folders

Import Python packages

import os
import warnings
import pathlib

warnings.filterwarnings('ignore')

Initialization

• Choose a country and add its name and country code

• Choose the variable to analyze (PM10, PM25, NO2, O3, etc.)

• Choose the area for your analysis

Choose the country of interest

country_code = 'IT' 
country_fullname = "Italy"
town_fullname = 'Venice'
town_coordinates = {'latitude': 45.4408, 'longitude': 12.3155}
variable_name = 'NO2'
variable_unit = 'kg m-3'
variable_long_name = 'Nitrogen Dioxide'

Geojson for selecting data from ADAM

• The geometry field is extracted from a GeoJSON file, retrieving the value of the “feature” element.

• To create a geojson file for the area of interest, you can use https://geojson.io/

• Then paste the result below in the geojson variable

geojson = """{ "type": "Feature", "properties": { }, 
            "geometry": {"type":"MultiPolygon",
                         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Create folders

WORKDIR_FOLDER = os.path.join(os.environ['HOME'], "datahub/Reliance/Climate" + '_' + country_code + '_' + variable_name)
print("WORKDIR FOLDER: ", WORKDIR_FOLDER)

WORKDIR FOLDER:  /home/jovyan/datahub/Reliance/Climate_IT_NO2

INPUT_DATA_DIR = os.path.join(WORKDIR_FOLDER, 'input')
OUTPUT_DATA_DIR = os.path.join(WORKDIR_FOLDER, 'output')
TOOL_DATA_DIR = os.path.join(WORKDIR_FOLDER, 'tool')

list_folders = [INPUT_DATA_DIR, OUTPUT_DATA_DIR, TOOL_DATA_DIR]

for folder in list_folders:
    pathlib.Path(folder).mkdir(parents=True, exist_ok=True)

Geojson for selecting data from ADAM

• We dissolve geojson in case we have more than one polygon and then save the results into a geojson file

import geopandas as gpd

local_path_geom = os.path.join(INPUT_DATA_DIR, country_code.lower() + '.geo.json')
local_path_geom

'/home/jovyan/datahub/Reliance/Climate_IT_NO2/input/it.geo.json'

if (pathlib.Path(local_path_geom).exists()):
    os.remove(local_path_geom)
f = open(local_path_geom, "w")
f.write(geojson)
f.close()

data = gpd.read_file(local_path_geom)

single_shape = data.dissolve()

Show area of interest

single_shape.plot()

<AxesSubplot:>

if (pathlib.Path(local_path_geom).exists()):
    os.remove(local_path_geom)

single_shape.to_file(local_path_geom, driver='GeoJSON')

Step 2: Authentication

The following lines of code will show the personal Adam API-Key of the user and the endpoint currently in use, that provides access to the products in the related catalogue. At the end of the execution, if the authentication process is successfull the personal token and the expiration time should be returned as outputs.

pip install adamapi

WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied: adamapi in /srv/conda/envs/notebook/lib/python3.9/site-packages (2.0.11)
Requirement already satisfied: imageio in /srv/conda/envs/notebook/lib/python3.9/site-packages (from adamapi) (2.9.0)
Requirement already satisfied: requests>=2.22.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from adamapi) (2.26.0)
Requirement already satisfied: charset-normalizer~=2.0.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests>=2.22.0->adamapi) (2.0.0)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests>=2.22.0->adamapi) (2021.10.8)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests>=2.22.0->adamapi) (3.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests>=2.22.0->adamapi) (1.26.7)
Requirement already satisfied: pillow in /srv/conda/envs/notebook/lib/python3.9/site-packages (from imageio->adamapi) (8.4.0)
Requirement already satisfied: numpy in /srv/conda/envs/notebook/lib/python3.9/site-packages (from imageio->adamapi) (1.20.0)
Note: you may need to restart the kernel to use updated packages.

adam_key = open(os.path.join(os.environ['HOME'],"adam-key")).read().rstrip()

import adamapi as adam
a = adam.Auth()

a.setKey(adam_key)
a.setAdamCore('https://reliance.adamplatform.eu')
a.authorize() 

{'expires_at': '2022-01-24T09:34:28.077Z',
 'access_token': 'a5ac0f1b57024109988940342b057200',
 'refresh_token': '57152366f5cc475a8c23eb12de0ce55d',
 'expires_in': 3600}

Step 3: Datasets Discovery

After authorization, the user can browse the whole catalogue, structured as a JSON object after a pagination process, displaying all the available datasets. This operation can be executed with the getDatasets() function without including any argument. Some lines of code should be added to parse the Json object and extract the names of the datasets.The Json object can be handled as a Python dictionary.

Pre-filter datasets

We will discover all the available datasets in the ADAM platform but will only print elements of interest EU_CAMS e.g. European air quality datasets from Copernicus Atmosphere Monitoring Service

def list_datasets(a, search="", dataset_name=""):
    datasets = adam.Datasets(a)
    catalogue = datasets.getDatasets()
    datasetID = None

# Extracting the size of the catalogue

    total = catalogue['properties']['totalResults']
    items = catalogue['properties']['itemsPerPage']
    pages = total // items
    
    print('\033[1;34m')
    print('----------------------------------------------------------------------')
    print( 'List of available datasets:')
    print ('\033[0;0m')

# Extracting the list of datasets across the whole catalogue

    for i in range(0, pages):
        page = datasets.getDatasets(page=i)
        for element in page['content']:
            if search == "" or search in element['title']:
                print(element['title'] + " --> datasetId = " + element['datasetId'])
                if element['title'] == dataset_name:
                    datasetID = element['datasetId']
    return datasets, datasetID

datasets, datasetID = list_datasets(a, search="EU_CAMS", dataset_name = 'EU_CAMS_SURFACE_' + variable_name + '_G')

----------------------------------------------------------------------
List of available datasets:

EU_CAMS_SURFACE_C2H3NO5_G --> datasetId = 69619:EU_CAMS_SURFACE_C2H3NO5_G
EU_CAMS_SURFACE_CO_G --> datasetId = 69620:EU_CAMS_SURFACE_CO_G
EU_CAMS_SURFACE_NH3_G --> datasetId = 69621:EU_CAMS_SURFACE_NH3_G
EU_CAMS_SURFACE_NMVOC_G --> datasetId = 69622:EU_CAMS_SURFACE_NMVOC_G
EU_CAMS_SURFACE_NO2_G --> datasetId = 69623:EU_CAMS_SURFACE_NO2_G
EU_CAMS_SURFACE_NO_G --> datasetId = 69624:EU_CAMS_SURFACE_NO_G
EU_CAMS_SURFACE_O3_G --> datasetId = 69625:EU_CAMS_SURFACE_O3_G
EU_CAMS_SURFACE_PM10_G --> datasetId = 69626:EU_CAMS_SURFACE_PM10_G
EU_CAMS_SURFACE_PM25_G --> datasetId = 69627:EU_CAMS_SURFACE_PM25_G
EU_CAMS_SURFACE_REC_G --> datasetId = 69628:EU_CAMS_SURFACE_REC_G
EU_CAMS_SURFACE_SIA_G --> datasetId = 69629:EU_CAMS_SURFACE_SIA_G
EU_CAMS_SURFACE_SO2_G --> datasetId = 69630:EU_CAMS_SURFACE_SO2_G
EU_CAMS_SURFACE_TEC_G --> datasetId = 69631:EU_CAMS_SURFACE_TEC_G

We are interested by one variable only so we will discover the corresponding dataset and print its metadata, showing the data provenance.

print('\033[1;34m' + 'Metadata of ' + datasetID + ':')
print ('\033[0;0m')

paged = datasets.getDatasets(datasetID)
for i in paged.items():
    print(str(i[0]) + ': ' + str(i[1]))

Metadata of 69623:EU_CAMS_SURFACE_NO2_G:

datasetId: 69623:EU_CAMS_SURFACE_NO2_G
creationDate: 2021-07-12T00:00:00Z
dataType: Float32
epsg: 4326
keywords: []
license: {'documentationUrl': '', 'dataProviderName': 'ADS', 'dataProviderUrl': '', 'licenseId': '', 'dataPolicy': '', 'doi': '', 'credits': ''}
maxValue: [1.354510459350422e-07]
minValue: [0.0]
numberOfRecords: 123782
profile: {'profileSchema': 'eo_profile_schema.json', 'name': 'Earth Observation', 'mission': 'CAMS', 'sensor': 'CAMS', 'processingLevel': 'forecast', 'instrument': '', 'platform': ''}
resolutionUnit: degree
temporalResolution: Hourly
unit: 
unitDescription: 
updateDate: 2022-01-23T12:07:34Z
geometry: {'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}
resolutions: [0.1]
anyText: 4326,ESA,Daily,ESA
applications: ['Atmosphere']
datasetManager: govoni@meeo.it
datasetManagerOrganisation: meeo
description: CAMS NITROGEN DIOXIDE
title: EU_CAMS_SURFACE_NO2_G
noDataValue: 0
timeReferenceSystem: UTC
units: µg m-3
unitsDescription: nitrogen dioxide
services: ['MWCS', 'ADAM', 'AdamApi']
technicalManager: govoni@meeo.it
filtersEnabled: {'type': 'object', 'title': 'Dataset filters', 'properties': {'startDate': {'title': 'Start Date', 'type': 'string', 'format': 'date', 'text_rule': 'false', 'ops_only': 'false', 'math_rule': 'false', 'order_rule': 'false', 'pattern': '^d{4}-[01]d-[0-3]d(T[0-2]d:[0-9]d:[0-9]dZ)?$'}, 'endDate': {'title': 'End Date', 'type': 'string', 'format': 'date', 'ops_only': 'false', 'text_rule': 'false', 'math_rule': 'false', 'order_rule': 'false', 'pattern': '^d{4}-[01]d-[0-3]d(T[0-2]d:[0-9]d:[0-9]dZ)?$'}}}
starDate: 2018-07-12T00:00:00Z
endDate: 2022-01-22T23:00:00Z
accounting: {'unit': 0.0032}

Step 4: Products Discovery

The products discovery operation related to a specific dataset is implemented in the Adam API with the getProducts() function. A combined spatial and temporal search can be requested by specifying the datasetId for the selected dataset, the geometry argument that specifies the Area Of Interest, and a temporal range defined by startDate and endDate . The geometry must always be defined by a GeoJson object that describes the polygon in the counterclockwise winding order. The optional arguments startIndex and maxRecords can set the list of the results returned as an output. The results of the search are displayed with their metadata and they are sorted starting from the most recent product.

Search data

pip install geojson_rewind

WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied: geojson_rewind in /srv/conda/envs/notebook/lib/python3.9/site-packages (1.0.2)
Note: you may need to restart the kernel to use updated packages.

from geojson_rewind import rewind
import json

The GeoJson object needs to be rearranged according to the counterclockwise winding order. This operation is executed in the next few lines to obtain a geometry that meets the requirements of the method. Geom_1 is the final result to be used in the discovery operation.

with open(local_path_geom) as f:
    geom_dict = json.load(f)
output = rewind(geom_dict)    
geom_1 = str(geom_dict['features'][0]['geometry'])

Copernicus air quality analyses are hourly product but when we select a given date, we will only get the first 10 products. Below, we make a list of the first 10 available products for the 1st September 2020 e.g. we restrict our search to this date.

start_date = '2019-09-01'
end_date = '2019-09-01'

search = adam.Search( a )
results = search.getProducts(
    datasetID, 
    geometry=geom_1,
    startDate=start_date,
    endDate=end_date
 )

# Printing the results

print('\033[1;34m' + 'List of available products (maximum 10 products printed):')
print ('\033[0;0m')

count = 1
for i in results['content']:
        print("\033[1;31;1m" + "#" + str(count))
        print ('\033[0m')
        for k in i.items():
            print(str(k[0]) + ': ' + str(k[1]))
        count = count+1
        print('------------------------------------')

List of available products (maximum 10 products printed):

#1

_id: {'$oid': '60efc2ae6dfebc080600365c'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T23:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901230000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#2

_id: {'$oid': '60efc2ae6dfebc0806003658'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T22:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901220000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#3

_id: {'$oid': '60efc2ae6dfebc0806003656'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T21:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901210000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#4

_id: {'$oid': '60efc2ae6dfebc0806003653'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T20:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901200000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#5

_id: {'$oid': '60efc2ae6dfebc080600364f'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T19:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901190000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#6

_id: {'$oid': '60efc2ae6dfebc080600364a'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T18:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901180000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#7

_id: {'$oid': '60efc2ae6dfebc0806003647'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T17:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901170000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#8

_id: {'$oid': '60efc2ae6dfebc0806003643'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T16:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901160000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#9

_id: {'$oid': '60efc2ae6dfebc080600363f'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T15:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901150000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------
#10

_id: {'$oid': '60efc2ae6dfebc080600363a'}
datasetId: EU_CAMS_SURFACE_NO2_G
productDate: 2019-09-01T14:00:00Z
productId: EU_CAMS_SURFACE_NO2_G_20190901140000.tif
geometry: {'geometries': [{'type': 'Polygon', 'coordinates': [[[-25.000012, 29.999997], [44.999988, 29.999997], [44.999988, 71.999997], [-25.000012, 71.999997], [-25.000012, 29.999997]]]}], 'type': 'GeometryCollection'}
insertDate: 2021-07-15T05:07:58Z
status: Online
------------------------------------

Step 5: Data Access

After the data discovery operation that retrieves the availability of products in the catalogue, it is possible to access the data with the getData function. Each product in the output list intersects the selected geometry and the following example shows how to access a specific product from the list of results obtained in the previous step. While the datasetId is always a mandatory parameter, for each data access request the getData function needs only one of the following arguments: geometry or productId , that is the value of the _id field in each product metadata. In the case of a spatial and temporal search the geometry must be provided to the function, together with the time range of interest. The output of the getData function is always a .zip file containing the data retrieved with the data access request, providing the spatial subset of the product. The zip file will contain a geotiff file for each of the spatial subsets extracted in the selected time range.

Define a function to select a time range and get data

def getZipData(auth, dataset_info):
    if not (pathlib.Path(pathlib.Path(dataset_info['outputFname']).stem).exists() or pathlib.Path(dataset_info['outputFname']).exists()):
        data=adam.GetData(auth)
        image = data.getData(
        datasetId = dataset_info['datasetID'],
        startDate = dataset_info['startDate'],
        endDate = dataset_info['endDate'],
        geometry = dataset_info['geometry'],
        outputFname = dataset_info['outputFname'])
        print(image)

Get variable of interest for each day of September 2019, 2020 and 2021 (time 00:00:00)

This process can take a bit of time so be patient!

import time
from IPython.display import clear_output

start = time.time()

for year in ['2019', '2020', '2021']:
    datasetInfo = {
    'datasetID' : datasetID,
    'startDate' : year + '-09-01',
    'endDate' : year + '-09-30',
    'geometry' : geom_1,
    'outputFname' : INPUT_DATA_DIR + '/' + variable_name + '_' + country_code + '_ADAMAPI_' + year + '.zip'
    }
    getZipData(a, datasetInfo)
    
end = time.time()
clear_output(wait=True)
delta1 = end - start
print('\033[1m'+'Processing time: ' + str(round(delta1,2)))

Processing time: 122.82

Step 6: Data Analysis and Visualization

The data retrieved via the Adam API is now available as a zip file that must be unzipped to directly handle the data in a geotiff format. Then with the Python packages provided in the Jupyter environment it is possible to process and visualized the requested product.

Unzip data

import zipfile

def unzipData(filename, out_prefix):
    with zipfile.ZipFile(filename, 'r') as zip_ref:
        zip_ref.extractall(path = os.path.join(out_prefix, pathlib.Path(filename).stem))

for year in ['2019', '2020', '2021']:
    filename = INPUT_DATA_DIR + '/' + variable_name + '_' + country_code + '_ADAMAPI_' + year + '.zip'
    target_file = pathlib.Path(os.path.join(INPUT_DATA_DIR, pathlib.Path(pathlib.Path(filename).stem)))
    if not target_file.exists():
        unzipData(filename, INPUT_DATA_DIR)

Read data and make a monthly average

import xarray as xr
import glob

We now read these files using xarray. First, we make a list of all the geotiff files in a given folder. To ensure each raster is labelled correctly with its time, we can use a helper function paths_to_datetimeindex() to extract time information from the file paths we obtained above. We then load and concatenate each dataset along the time dimension using xarray.open_rasterio(), convert the resulting xarray.DataArray to a xarray.Dataset, and give the variable a more useful name (PM10)

from datetime import datetime

def paths_to_datetimeindex(paths):
    return  [datetime.strptime(date.split('_')[-1].split('.')[0], '%Y-%m-%dt%f') for date in paths]

def getData(dirtif, variable):
    geotiff_list = glob.glob(dirtif)
    # Create variable used for time axis
    time_var = xr.Variable('time', paths_to_datetimeindex(geotiff_list))
    # Load in and concatenate all individual GeoTIFFs
    geotiffs_da = xr.concat([xr.open_rasterio(i, parse_coordinates=True) for i in geotiff_list],
                        dim=time_var)
    # Covert our xarray.DataArray into a xarray.Dataset
    geotiffs_da = geotiffs_da.to_dataset('band')
    # Rename the dimensions to make it CF-convention compliant
    geotiffs_da = geotiffs_da.rename_dims({'y': 'latitude', 'x':'longitude'})
    # Rename the variable to a more useful name
    geotiffs_da = geotiffs_da.rename_vars({1: variable, 'y':'latitude', 'x':'longitude'})

    return geotiffs_da

geotiff_ds = getData( INPUT_DATA_DIR + '/' + variable_name + '_'+ country_code + '_ADAMAPI_20*/*.tif', variable_name)
geotiff_ds[variable_name].attrs = {'units' : variable_unit, 'long_name' : variable_long_name }
geotiff_ds

<xarray.Dataset>
Dimensions:    (time: 90, latitude: 117, longitude: 120)
Coordinates:
  * latitude   (latitude) float64 47.05 46.95 46.85 46.75 ... 35.65 35.55 35.45
  * longitude  (longitude) float64 6.65 6.75 6.85 6.95 ... 18.35 18.45 18.55
  * time       (time) datetime64[ns] 2019-09-01 2019-09-02 ... 2021-09-30
Data variables:
    NO2        (time, latitude, longitude) float32 0.0 0.0 0.0 ... 0.0 0.0 0.0
Attributes:
    transform:      (0.1, 0.0, 6.599987990701003, 0.0, -0.1, 47.09999699761336)
    crs:            +init=epsg:4326
    res:            (0.1, 0.1)
    is_tiled:       0
    nodatavals:     (0.0,)
    scales:         (1.0,)
    offsets:        (0.0,)
    AREA_OR_POINT:  Area

Analyze data

Make yearly average for the month of September

geotiff_dm = geotiff_ds.groupby('time.year').mean('time', keep_attrs=True)

geotiff_dm

<xarray.Dataset>
Dimensions:    (year: 3, latitude: 117, longitude: 120)
Coordinates:
  * latitude   (latitude) float64 47.05 46.95 46.85 46.75 ... 35.65 35.55 35.45
  * longitude  (longitude) float64 6.65 6.75 6.85 6.95 ... 18.35 18.45 18.55
  * year       (year) int64 2019 2020 2021
Data variables:
    NO2        (year, latitude, longitude) float32 0.0 0.0 0.0 ... 0.0 0.0 0.0
Attributes:
    transform:      (0.1, 0.0, 6.599987990701003, 0.0, -0.1, 47.09999699761336)
    crs:            +init=epsg:4326
    res:            (0.1, 0.1)
    is_tiled:       0
    nodatavals:     (0.0,)
    scales:         (1.0,)
    offsets:        (0.0,)
    AREA_OR_POINT:  Area

Visualize data

pip install cmaps

WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied: cmaps in /srv/conda/envs/notebook/lib/python3.9/site-packages (1.0.5)
Requirement already satisfied: matplotlib in /srv/conda/envs/notebook/lib/python3.9/site-packages (from cmaps) (3.5.0)
Requirement already satisfied: numpy in /srv/conda/envs/notebook/lib/python3.9/site-packages (from cmaps) (1.20.0)
Requirement already satisfied: kiwisolver>=1.0.1 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (1.3.2)
Requirement already satisfied: pillow>=6.2.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (8.4.0)
Requirement already satisfied: fonttools>=4.22.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (4.28.2)
Requirement already satisfied: python-dateutil>=2.7 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (2.7.5)
Requirement already satisfied: cycler>=0.10 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (0.11.0)
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Requirement already satisfied: packaging>=20.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from matplotlib->cmaps) (21.3)
Requirement already satisfied: six>=1.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from python-dateutil>=2.7->matplotlib->cmaps) (1.16.0)
Note: you may need to restart the kernel to use updated packages.

import cartopy.crs as ccrs
import matplotlib.pyplot as plt
import cmaps

# To plot over Norway, taking a central longitude of 60 is fine. You may want to change it when plotting over different geographical areas
central_longitude = town_coordinates['latitude']

# generate figure
proj_plot = ccrs.Mercator(central_longitude=central_longitude)

lcmap = cmaps.BlueYellowRed
# Only plot values greater than 0
p = geotiff_dm[variable_name].where(geotiff_dm[variable_name] > 0).plot(x='longitude', y='latitude',
                                                                 transform=ccrs.PlateCarree(),
                                                                 subplot_kws={"projection": proj_plot},
                                                                 size=8,
                                                                 col='year', col_wrap=3, robust=True,
                                                                 cmap=lcmap, add_colorbar=True)

# We have to set the map's options on all four axes
for ax,i in zip(p.axes.flat,  geotiff_dm.year.values):
    ax.coastlines()
    ax.set_title('Surface ' + variable_name + '\n' + 'September ' + str(i), fontsize=10)

plot_file = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2019-2021.png')
if os.path.exists(plot_file + '.bak'):
    os.remove(plot_file + '.bak')
if os.path.exists(plot_file):
    os.rename(plot_file, plot_file + '.bak') 
plt.savefig(plot_file)

Plot one single date

fig=plt.figure(figsize=(10,10))
# Define the projection
crs=ccrs.PlateCarree()

# We're using cartopy and are plotting in Orthographic projection 
# (see documentation on cartopy)
ax = plt.subplot(1, 1, 1, projection=ccrs.Mercator(central_longitude=central_longitude))
ax.coastlines(resolution='10m')

# custom colormap

lcmap = cmaps.BlueYellowRed

# We need to project our data to the new Mercator projection and for this we use `transform`.
# we set the original data projection in transform (here PlateCarree)
# we only plot values greather than 0
img = geotiff_ds[variable_name].where(geotiff_ds[variable_name] > 0).sel(time='2021-09-15').plot(ax=ax,
                                                                                                 transform=ccrs.PlateCarree(),
                                                                                                 cmap=lcmap)  

# Title for plot
plt.title('Surface ' + variable_name + '\n 15th September 2021 over ' + country_fullname,
          fontsize = 16, fontweight = 'bold', pad=10)

plot_file = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2021-09-15.png')
if os.path.exists(plot_file + '.bak'):
    os.remove(plot_file + '.bak')
if os.path.exists(plot_file):
    os.rename(plot_file, plot_file + '.bak')  
plt.savefig(plot_file)

Interactive plot with bokeh

import holoviews as hv
import hvplot.xarray

Interactive plot from 1st September to 30th September 2021

geotiff_ds = geotiff_ds.sortby('time')

plot_start_time = '2021-09-01'
plot_end_time = '2021-09-30'
labels = geotiff_ds.hvplot.labels( text_font_size='6pt', text_color='blue').opts(xoffset=20)
map_hv = geotiff_ds.where(geotiff_ds[variable_name] > 0).sel(time=slice(plot_start_time, plot_end_time))[variable_name].hvplot(
    groupby="time",
    cmap=lcmap,
    geo=True,
    coastline='10m',
    frame_width=400,
    clim=(0,35) 
)
plot_file = os.path.join(OUTPUT_DATA_DIR, "interactive_map_" + plot_start_time + "_" + plot_end_time + ".html")
if os.path.exists(plot_file + '.bak'):
    os.remove(plot_file + '.bak')
if os.path.exists(plot_file):
    os.rename(plot_file, plot_file + '.bak') 
hv.save(map_hv, plot_file, backend="bokeh")

Save Data Cube selection into netCDF

output_file = os.path.join(OUTPUT_DATA_DIR, variable_name + "_september_" + country_code + "_2019-2021.nc")
if os.path.exists(output_file + '.bak'):
    os.remove(output_file + '.bak')
if os.path.exists(output_file):
    os.rename(output_file, output_file + '.bak') 
geotiff_ds.to_netcdf(output_file)

Plot a timeseries

Timeseries from 1st September to 30th September 2021

Sort times and then select one location

# You may change this location accordingly
location = town_fullname
latitude = town_coordinates['latitude']
longitude = town_coordinates['longitude']
plot_end_time = '2021-09-01'
plot_end_time = '2021-09-30'

ts = geotiff_ds[variable_name].where(geotiff_ds[variable_name] > 0). \
        sel(latitude=latitude, longitude=longitude, method='nearest'). \
        sel(time=slice(plot_start_time, plot_end_time))

ts_plot = ts.hvplot(color='purple') * ts.hvplot.scatter(marker='o', color='blue', size=15)

ts_plot

plot_file = os.path.join(OUTPUT_DATA_DIR, "interactive_timeseries_" + location + "_" + plot_start_time + "_" + plot_end_time + ".html")
if os.path.exists(plot_file + '.bak'):
    os.remove(plot_file + '.bak')
if os.path.exists(plot_file):
    os.rename(plot_file, plot_file + '.bak') 
hv.save(ts_plot, plot_file, backend="bokeh")

Save timeseries into tabular (csv) file

output_file = os.path.join(OUTPUT_DATA_DIR, "timeseries_" + location + "_september2021.csv")
if os.path.exists(output_file + '.bak'):
    os.remove(output_file + '.bak')
if os.path.exists(output_file):
    os.rename(output_file, output_file + '.bak') 
ts.to_series().to_csv(output_file, sep='\t')

Step 7: Create Research Object and Share my work

pip install rohub

WARNING: The directory '/home/jovyan/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Requirement already satisfied: rohub in /srv/conda/envs/notebook/lib/python3.9/site-packages (1.0.2)
Requirement already satisfied: pandas in /srv/conda/envs/notebook/lib/python3.9/site-packages (from rohub) (1.3.4)
Requirement already satisfied: requests in /srv/conda/envs/notebook/lib/python3.9/site-packages (from rohub) (2.26.0)
Requirement already satisfied: python-dateutil>=2.7.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (2.7.5)
Requirement already satisfied: pytz>=2017.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (2021.3)
Requirement already satisfied: numpy>=1.17.3 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from pandas->rohub) (1.20.0)
Requirement already satisfied: six>=1.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from python-dateutil>=2.7.3->pandas->rohub) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (2021.10.8)
Requirement already satisfied: idna<4,>=2.5 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (3.1)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (1.26.7)
Requirement already satisfied: charset-normalizer~=2.0.0 in /srv/conda/envs/notebook/lib/python3.9/site-packages (from requests->rohub) (2.0.0)
Note: you may need to restart the kernel to use updated packages.

import os
import pathlib
from rohub import rohub, settings

Authenticating

• If the code cell below fails, make sure you have created the two files:

  • rohub-user: contains your rohub username

  • rohub-pwd: contains your rohub password

rohub_user = open(os.path.join(os.environ['HOME'],"rohub-user")).read().rstrip()
rohub_pwd = open(os.path.join(os.environ['HOME'],"rohub-pwd")).read().rstrip()

rohub.login(username=rohub_user, password=rohub_pwd)

Logged successfully as annefou@geo.uio.no.

Create a new Exectuable RO

ro_title = variable_name + ' in ' + country_fullname + " Jupyter notebook demonstrating the usage of CAMS European air quality analysis from Copernicus Atmosphere Monitoring with RELIANCE services" 
ro_research_areas = ["Earth sciences"]
ro_description = "This Research Object demonstrates how to use CAMS European air quality analysis from Copernicus Atmosphere Monitoring with RELIANCE services and compute monthly map of " + \
                 variable_name + "over a given geographical area, here " + country_fullname
ro = rohub.ros_create(title=ro_title, research_areas=ro_research_areas, 
                      description=ro_description, 
                      use_template=True,
                      ros_type="Executable Research Object")

Research Object was successfully created with id = e4e9e394-aca5-4a87-a5c1-199d6577371e

Show metadata

ro.show_metadata()

{'identifier': 'e4e9e394-aca5-4a87-a5c1-199d6577371e',
 'shared_link': 'https://w3id.org/ro-id/e4e9e394-aca5-4a87-a5c1-199d6577371e',
 'title': 'NO2 in Italy Jupyter notebook demonstrating the usage of CAMS European air quality analysis from Copernicus Atmosphere Monitoring with RELIANCE services',
 'description': 'This Research Object demonstrates how to use CAMS European air quality analysis from Copernicus Atmosphere Monitoring with RELIANCE services and compute monthly map of NO2over a given geographical area, here Italy',
 'status': 'LIVE',
 'access_mode': 'PUBLIC',
 'type': 'Executable Research Object',
 'template': 'Executable Research Object folders structure',
 'created': '2022-01-24T08:41:42.603825Z',
 'creator': 'annefou@geo.uio.no',
 'modificator': None,
 'modified': '2022-01-24T08:41:43.082955Z',
 'importer': None,
 'research_areas': ['Earth sciences'],
 'owner': 'annefou@geo.uio.no',
 'editors': [],
 'readers': [],
 'rating': '0.00',
 'number_of_ratings': 0,
 'number_of_likes': 0,
 'number_of_dislikes': 0,
 'quality': 0,
 'size': 0,
 'creation_mode': 'MANUAL',
 'doi': None,
 'api_link': 'https://api.rohub.org/api/ros/e4e9e394-aca5-4a87-a5c1-199d6577371e/'}

Add additional authors and/or contributors to our Research Object

ro.set_authors(agents=author_emails)

Agent: annefou@geo.uio.no recognized in the system.
Agent: jeani@uio.no recognized in the system.

[{'identifier': '62277187-0f2e-4320-a6b0-7fe467f1b1c1',
  'username': 'annefou@geo.uio.no',
  'name': 'annefou@geo.uio.no',
  'type': 'RohubUser',
  'display_name': 'Anne Fouilloux',
  'orcid_identifier': '0000-0002-1784-2920',
  'affiliation': 'Nordic e-Infrastructure Collaboration (NeIC)'},
 {'identifier': '1ac03644-c78c-4ca2-b0b4-2d9e40f671af',
  'username': 'jeani@uio.no',
  'name': 'jeani@uio.no',
  'type': 'ExternalUser',
  'display_name': 'Jean Iaquinta',
  'orcid_identifier': '0000-0002-8763-1643',
  'affiliation': 'UiO'}]

Add publisher/copyright holder

• Use Research Organization Registry (ROR) to find the identifier of your organization

Add publishers

ro.set_publishers(agents=list_publishers)

Agent: {'org_id': 'http://www.uio.no/english/', 'display_name': 'University of Oslo', 'agent_type': 'organization', 'ror_identifier': '01xtthb56', 'organization_url': 'http://www.uio.no/english/'} recognized in the system.
Agent: {'org_id': 'https://neic.no/', 'display_name': 'Nordic e-Infrastructure Collaboration', 'agent_type': 'organization', 'ror_identifier': '04jcwf484', 'organization_url': 'https://neic.no/'} recognized in the system.

[{'identifier': '1d581e9d-25e2-4029-bdeb-6c055a0db8e4',
  'username': 'https://ror.org/01xtthb56',
  'name': 'https://ror.org/01xtthb56',
  'type': 'Organization',
  'display_name': 'University of Oslo'},
 {'identifier': 'fbd9bdcf-4a1d-4ae8-9a90-6b9ec5a3b8b2',
  'username': 'https://ror.org/04jcwf484',
  'name': 'https://ror.org/04jcwf484',
  'type': 'Organization',
  'display_name': 'Nordic e-Infrastructure Collaboration'}]

ro.set_copyright_holders(agents=list_copyright_holders)

Agent: {'org_id': 'http://www.uio.no/english/', 'display_name': 'University of Oslo', 'agent_type': 'organization', 'ror_identifier': '01xtthb56', 'organization_url': 'http://www.uio.no/english/'} recognized in the system.

[{'identifier': '1d581e9d-25e2-4029-bdeb-6c055a0db8e4',
  'username': 'https://ror.org/01xtthb56',
  'name': 'https://ror.org/01xtthb56',
  'type': 'Organization',
  'display_name': 'University of Oslo'}]

organizations = rohub.organizations_find()
organizations

	identifier	organization_id	display_name	email	url	ror_identifier
0	9196f718-5be7-40da-a64e-6c6c8928b826	example_orgA@email.com	(example)Organization A	example_orgA@email.com	None	None
1	92459295-cc33-40a2-b2ca-e416ad73a95e	neworg_1@example.org	Example Org 1	neworg1@example.org	http://neworg1.example.org	abcd123
2	556f3671-87b4-4576-b39d-654942ef248e	neworg_2@example.org	Example Org 2	neworg2@example.org	http://neworg2.example.org	abcd123
3	fbd9bdcf-4a1d-4ae8-9a90-6b9ec5a3b8b2	https://ror.org/04jcwf484	Nordic e-Infrastructure Collaboration	None	https://neic.no/	04jcwf484
4	b1893a50-9f9b-49e8-8ab7-114152e29b9e	https://neic.no/	Nordic e-Infrastructure Collaboration		https://neic.no/	04jcwf484
5	64ec5402-1171-42f6-b9dd-6fa901ca9724	https://ror.org/025cj6e44	Poznan Supercomputing and Networking Center	office@man.poznan.pl	https://www.psnc.pl/	025cj6e44
6	f8b4ad0c-a4b1-4595-81a0-dcf42db083d4	http://www.uio.no/english/	University of Oslo		http://www.uio.no/english/	01xtthb56
7	1d581e9d-25e2-4029-bdeb-6c055a0db8e4	https://ror.org/01xtthb56	University of Oslo	None	http://www.uio.no/english/	01xtthb56

Add RO Funding information

if funded_by:
    ro.add_funding(grant_identifier=funded_by["grant_id"], grant_name=funded_by["grant_Name"],
                   funder_name=funded_by["funder_name"], grant_title=funded_by["grant_title"],
                   funder_doi=funded_by["funder_doi"])

Add RO license

ro.set_license(license_id=license) 

{'identifier': 'MIT',
 'title': 'MIT License',
 'description': 'MIT License',
 'created': '2016-09-12T02:51:35.895509+00:00',
 'updated': '2021-10-07T08:21:23.483114+00:00',
 'creator': None,
 'status': 'active',
 'url': 'https://opensource.org/licenses/MIT',
 'custom': False}

Aggregate Resources

• We will be adding all the resources generated by our notebook (data and plots)

• Our data and plots can also be shared in B2DROP so we will get the shared link from B2DROP and add it to our research object

List RO folders for this type of RO

myfolders = ro.list_folders()
myfolders

	identifier	name	description	creator	created_on	modified_on	path
0	0932dec9-d3f3-467d-bd8c-e331e9ee12dc	biblio	None	annefou@geo.uio.no	2022-01-24T08:41:43.319743+0000	2022-01-24T08:41:43.320820+0000	biblio
1	6a363936-7eaf-433d-b2d4-c608328a6056	input	None	annefou@geo.uio.no	2022-01-24T08:41:43.319886+0000	2022-01-24T08:41:43.321252+0000	input
2	c4a13ce4-35a6-4e5d-9e9f-8bd3abf2a43c	output	None	annefou@geo.uio.no	2022-01-24T08:41:43.319970+0000	2022-01-24T08:41:43.321353+0000	output
3	0ed40e62-31a4-4875-a59d-ffba1e13d71d	tool	None	annefou@geo.uio.no	2022-01-24T08:41:43.320047+0000	2022-01-24T08:41:43.321421+0000	tool

Aggregate internal resources

Add sketch to my RO

res_file_path = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2019-2021.png')
res_res_type = "Sketch"
res_title = variable_long_name + " [" + variable_unit + "] over " + country_fullname + " for September 2019, 2020 and 2021"
res_description = "Monthly average maps of CAMS " + variable_long_name + " [" + variable_unit + "] over " + country_fullname + " in 2019, 2020 and 2021"
res_folder =  myfolders[myfolders['name'] == 'output'].iloc[0]['identifier']

ro.add_internal_resource(res_type=res_res_type, file_path=res_file_path, title=res_title, description=res_description, folder=res_folder)

Resource was successfully created with id = 439c7983-72f9-4210-ba86-cecbeeb0f284

Resource(identifier=439c7983-72f9-4210-ba86-cecbeeb0f284, post_request=False)

Aggregate external resources

Get shared link from datahub

1. Retrieve your client identifier, client secret and refresh token from https://aai.egi.eu/fedcloud/

2. Create a new file in your HOME area for instance using nano (keep the $ character in front of HOME; this is meant to be an environment variable):

nano $HOME/egi_fedcloud.cfg

1. Paste your client identifier, client secret and refresh token using the following syntax (do not forget { and } as well as comma , and columns :

{
"id": "XXXXXXXXXXXXXXXXX",
"secret": "YYYYYYYYYYYYYYYYYYYYYYYYYYYYYYY",
"token": "ffffffffffffffffffffffff"
}

1. You are ready to go. If you have issues, check first that the syntax is correct in your egi_fedcloud.cfg, that this file is located in the correct folder and then finally that your refresh token is still valid (check on https://aai.egi.eu/fedcloud/)

import os
import json
import requests
import datetime
import shutil

EGI Datahub functions to initialize EGI datahub and get shared link

def egi_datahub_init():
    egi_fedcloud_filename = os.path.join(os.environ['HOME'], 'egi_fedcloud.cfg')
    with open(egi_fedcloud_filename, 'r') as convert_file:
        tmp = convert_file.read()
        egi_fedcloud_auth = json.loads(tmp)
        try:
            # Retrieving an OIDC token from Check-in
            data = {
                'client_id': egi_fedcloud_auth['id'],
                'client_secret': egi_fedcloud_auth['secret'],
                'refresh_token': egi_fedcloud_auth['token'],
                'scope': 'openid email profile',
                'grant_type': 'refresh_token'
            }
            response = requests.post('https://aai.egi.eu/oidc/token', data=data, auth=(egi_fedcloud_auth['id'], 
                                                                                       egi_fedcloud_auth['secret']))
            #print(json.dumps(response.json(), indent=2))
            EGItoken = response.json()['access_token']
            headers = {
                'X-Auth-Token': f"egi:" + EGItoken,
                'Content-type': 'application/json',
            }
            # get current timestamp
            ts = datetime.datetime.now().timestamp()
            data = json.dumps({ 
                'name': 'REST and CDMI access token ' + str(ts), 
                'type': { 
                    'accessToken': {} 
                }, 
                'caveats': [ { 
                    'type': 'interface', 
                    'interface': 'rest' 
                }] 
            })

            response = requests.post('https://datahub.egi.eu/api/v3/onezone/user/tokens/named', headers=headers, data=data)
            DATAHUB_TOKEN = response.json()['token']
            return DATAHUB_TOKEN
        except:
            print("EGI Datahub Authentication problem: check your credentials")

def egi_datahub_getlink(datahub_token, filename):
    bname = os.path.basename(filename)
    datahub_remote_prefix = 'https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/'
    hname = filename.split('datahub/')[1]
    datahub_location = os.path.join(datahub_remote_prefix, hname)
    print(datahub_location)
    headers = { 'X-Auth-Token': datahub_token }
    response = requests.get(datahub_location, headers=headers)
    dh_fileid = response.json()[0]['id']
    
    headers = { 'X-Auth-Token': datahub_token, 'Content-Type': 'application/json',}
    data = json.dumps({ 'name': bname,
    'fileId': dh_fileid
    })
    response = requests.post('https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/shares', headers=headers, data=data)
    # print(json.dumps(response.json(), indent=2))
    shareIdGenerated=response.json()['shareId']
    
    headers = {'X-Auth-Token': datahub_token}
    response = requests.get('https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/shares/'+shareIdGenerated, headers=headers) 
    # print(json.dumps(response.json(), indent=2))
    publicURL = response.json()['publicUrl']
    return publicURL

EGI DataHub initialization

DATAHUB_TOKEN = egi_datahub_init()

Add inputs to my RO

• I used ADAM to retrieve relevant data but I will be sharing what I retrieved from the data cube so that my collaborators do not have to re-download the same input data again.

Geojson file used for rertieving data from ADAM data-cube

shared_input_path = os.path.join(INPUT_DATA_DIR, country_code.lower() + '.geo.json')
print(shared_input_path)
res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_input_path)
res_type = "Dataset"
res_title = "Geojson for " + country_fullname
res_description = "Geojson file used for retrieving data from the ADAM platform over " + country_fullname
res_folder = myfolders[myfolders['name'] == 'input'].iloc[0]['identifier']
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

/home/jovyan/datahub/Reliance/Climate_IT_NO2/input/it.geo.json
https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/input/it.geo.json
Resource was successfully created with id = 8d7b15a5-2958-4d6d-9f7a-1e326ea508af

Resource(identifier=8d7b15a5-2958-4d6d-9f7a-1e326ea508af, post_request=False)

Input data retrieved from ADAM data-cube

for year in ['2019', '2020', '2021']:
    shared_input_path = os.path.join(INPUT_DATA_DIR, variable_name + '_' + country_code + '_ADAMAPI_' + year + '.zip')
    print(shared_input_path)
    res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_input_path)
    res_type = "Data Cube Product"
    res_title = "Data-Cube from ADAM platform over " + country_fullname + " in September " + year
    res_description = "This dataset is a data-Cube retrieved from the ADAM platform over " + country_fullname + " in September " + year
    res_folder = myfolders[myfolders['name'] == 'input'].iloc[0]['identifier']
    ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

/home/jovyan/datahub/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2019.zip
https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2019.zip
Resource was successfully created with id = ca5e9c9f-e70a-41c0-bf46-613a2d64e5af
/home/jovyan/datahub/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2020.zip
https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2020.zip
Resource was successfully created with id = 6030bf35-b775-4b84-8647-8dfbc3066992
/home/jovyan/datahub/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2021.zip
https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/input/NO2_IT_ADAMAPI_2021.zip
Resource was successfully created with id = f5cf0711-5004-47ab-a773-f74eb1173b91

Add our Jupyter Notebook to our RO

• Make a copy of the current notebook to the tool folder for sharing as an external resource

notebook_filename = 'RELIANCE_' + country_fullname + '_' + variable_name + '.ipynb'
local_notebook_path = os.path.join('./', notebook_filename)
shared_notebook_path = os.path.join(TOOL_DATA_DIR, notebook_filename)

shared_notebook_path

'/home/jovyan/datahub/Reliance/Climate_IT_NO2/tool/RELIANCE_Italy_NO2.ipynb'

Copy current notebook to shared datahub

bkfile = shared_notebook_path + '.bak'
if os.path.exists(bkfile):
    os.remove(bkfile)
if os.path.exists(shared_notebook_path):
    os.rename(shared_notebook_path, bkfile)
shutil.copy2(local_notebook_path, shared_notebook_path)

'/home/jovyan/datahub/Reliance/Climate_IT_NO2/tool/RELIANCE_Italy_NO2.ipynb'

Create a shared link for my Jupyter Notebook

Get public URL from EGI Datahub to share link in RO

res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_notebook_path)
res_type = "Jupyter Notebook"
res_title = "Jupyter Notebook of CAMS European air quality analysis from Copernicus Atmosphere Monitoring with RELIANCE services - Applied over " + country_fullname + " and variable " + variable_long_name
res_description = "Jupyter Notebook for discovering, accessing and processing RELIANCE data cube, and creating a Research Object with results, and finally publish it in Zenodo"
res_folder = myfolders[myfolders['name'] == 'tool'].iloc[0]['identifier']
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/tool/RELIANCE_Italy_NO2.ipynb
Resource was successfully created with id = 53c79245-d419-41a1-9b01-de0ad9aa1504

Resource(identifier=53c79245-d419-41a1-9b01-de0ad9aa1504, post_request=False)

Add first plot as Image to my Research Object (external resource from EGI Datahub)

shared_plot_path = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2019-2021.png')
print(shared_plot_path)
res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_plot_path)
res_type = "Image"
res_title = variable_long_name + " [" + variable_unit + "] over " + country_fullname + " for September 2019, 2020 and 2021"
res_description = "Monthly average maps of CAMS " + variable_long_name + " [" + variable_unit + "] over " + country_fullname + " in 2019, 2020 and 2021"
res_folder = myfolders[myfolders['name'] == 'output'].iloc[0]['identifier']
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

/home/jovyan/datahub/Reliance/Climate_IT_NO2/output/NO2_september_IT_2019-2021.png
https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/output/NO2_september_IT_2019-2021.png
Resource was successfully created with id = 6264c945-c7ba-476e-9a17-d1bcafea73db

Resource(identifier=6264c945-c7ba-476e-9a17-d1bcafea73db, post_request=False)

Add second plot as Image to my Research Object (external resource from EGI Datahub)

shared_plot_path = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2021-09-15.png')
res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_plot_path)
res_type = "Image"
res_title = variable_long_name + " [" + variable_unit + "] over " + country_fullname + " on September 15, 2021"
res_description="Daily average maps of CAMS " + variable_long_name + variable_unit + "] over " + country_fullname + " on September 15, 2021"
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/output/NO2_september_IT_2021-09-15.png
Resource was successfully created with id = 3731a0a3-92bd-44ab-81e8-d548ac004206

Resource(identifier=3731a0a3-92bd-44ab-81e8-d548ac004206, post_request=False)

Add timeseries for the town (external resource from EGI Datahub)

shared_plot_path = os.path.join(OUTPUT_DATA_DIR, 'timeseries_' + town_fullname + '_september2021.csv')
res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_plot_path)
res_type="Result"
res_title="Timeseries of " + variable_long_name + " [" + variable_unit + "] over " + town_fullname + " in september 2021"
res_description="Daily average of CAMS " + variable_long_name + variable_unit + "] over " + town_fullname + " in September 2021"
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/output/timeseries_Venice_september2021.csv
Resource was successfully created with id = b1e060ff-ec18-44e9-842a-cae4d1e7d265

Resource(identifier=b1e060ff-ec18-44e9-842a-cae4d1e7d265, post_request=False)

Add netCDF file corresponding to Data cube selection (external resource from EGI Datahub)

shared_plot_path = os.path.join(OUTPUT_DATA_DIR, variable_name + '_september_' + country_code + '_2019-2021.nc')
res_file_url = egi_datahub_getlink(DATAHUB_TOKEN, shared_plot_path)
res_type="Result"
res_title="netCDF data for daily " + variable_name + "over " + country_fullname + " in September 2019, 2020 and 2021"
res_description="netCDF data corresponding to daily average of CAMS " + variable_long_name + " [" + variable_unit + "] over " + country_fullname + " for September 2019, September 2020 and September 2021"
ro.add_external_resource(res_type=res_type, input_url=res_file_url, title=res_title, description=res_description, folder=res_folder)

https://cesnet-oneprovider-01.datahub.egi.eu/api/v3/oneprovider/files/Reliance/Climate_IT_NO2/output/NO2_september_IT_2019-2021.nc
Resource was successfully created with id = 45fc98ad-daa0-475f-9262-55a75a90f59d

Resource(identifier=45fc98ad-daa0-475f-9262-55a75a90f59d, post_request=False)

Additional metadata for the RO

Add geolocation to my Research Object

• We need to transform our geojson file into geojson-ld

from geojson_rewind import rewind
import json

geojson_ld_file = os.path.join(INPUT_DATA_DIR, country_code.lower() + '.geo-ld.json')
bkfile = geojson_ld_file + '.bak'
if os.path.exists(bkfile):
    os.remove(bkfile)
if os.path.exists(geojson_ld_file):
    os.rename(geojson_ld_file, bkfile)
shutil.copy2(os.path.join(INPUT_DATA_DIR, country_code.lower() + '.geo.json'), geojson_ld_file)

with open(geojson_ld_file , 'r+') as f:
    data = json.load(f)
    output = rewind(data)
    output['@context'] = { "geojson": "https://purl.org/geojson/vocab#" } 
    f.seek(0)        
    json.dump(output, f, indent=None)
    f.truncate()

geolocation_file_path = os.path.join(INPUT_DATA_DIR, country_code.lower() + '.geo.json')
ro.add_geolocation(body_specification_json=geolocation_file_path)

[{'identifier': '9e2dee49-402d-4ac3-adca-da5c64cdfc17',
  'shared_link': 'https://w3id.org/ro-id/e4e9e394-aca5-4a87-a5c1-199d6577371e/annotations/9e2dee49-402d-4ac3-adca-da5c64cdfc17',
  'name': 'annotations/9e2dee49-402d-4ac3-adca-da5c64cdfc17',
  'filename': '.ro/annotations/9e2dee49-402d-4ac3-adca-da5c64cdfc17.ttl',
  'relation': False,
  'read_only': False,
  'target': 'e4e9e394-aca5-4a87-a5c1-199d6577371e',
  'ro': 'e4e9e394-aca5-4a87-a5c1-199d6577371e',
  'resources': [],
  'created': '2022-01-24T08:42:23.388809+0000',
  'creator': 'annefou@geo.uio.no',
  'modificator': None,
  'modified': '2022-01-24T08:42:23.388725+0000',
  'authors_credits': ['annefou@geo.uio.no'],
  'contributors_credits': [],
  'api_link': 'https://api.rohub.org/api/annotations/9e2dee49-402d-4ac3-adca-da5c64cdfc17/'}]

Export to RO-crate

ro.export_to_rocrate(filename="climate_EU-CAMS_" + country_code + "_" + variable_name + "_ro-crate", use_format="zip")

File was successfully downloaded.

Take a snapshot of my RO

#snapshot_id=ro.snapshot()

Archive and publish to Zenodo, optionally assign DOI

snapshot_title="Jupyter Notebook Analysing the Air quality during Covid-19 pandemic using Copernicus Atmosphere Monitoring Service - Applied over " + country_fullname + " with " + variable_long_name
#snapshot_id_pub=ro.snapshot(title=snapshot_title, create_doi=True, publication_services=["Zenodo"])
#snapshot_id_pub

Load the published Research Object

#published_ro = rohub.ros_load(identifier=snapshot_id)

Show the DOI and get the link

#published_ro.show_publication()

Fork and reuse existing RO to create derivative work

#fork_id=ro.fork(title="Forked Jupyter Notebook to analyze  the Air quality during Covid-19 pandemic using Copernicus Atmosphere Monitoring Service")
#forked_ro = rohub.ros_load(identifier=fork_id)
#forked_ro.show_metadata()

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NO2 over Viken & Oslo (Norway) with CAMS European air quality analysis using RELIANCE services