Through this tutorial you will learn here how to access and download Copernicus Data Space Ecosystem (CDSE) data through a jupyterlab Galaxy interactive tool :

This tool enables you to leverage the Copernicus Data Space Ecosystem services and access data effortlessly. The JupyterLab service allows you to dive into data exploration, visualization, and analysis without the hassle of installing dependencies or downloading large data sets.

You will also apprehend how to use the Holoviz ecosysytem by plotting and visualising NDVI (from the CDSE) timeseries : HoloViz provides high-level Python tools that are designed to work together to solve the entire problem of visualization, from conducting exploratory data analysis to deploying complex dashboards.

Agenda

In this tutorial, we will cover:

1. Context on Galaxy
2. Copernicus Data Space Ecosystem
3. Holoviz
4. Conclusion

Context on Galaxy

Interactive tools work differently than classical tools as it allows the user to interact with a dedicated graphical interface. This kind of tools is used to give access to Jupyter notebooks, RStudio or R Shiny apps for example.

Details: Short introduction on how Galaxy works

You can come back to where you left off the tutorial anytime by clicking level.

Hands-on: Log in to Galaxy

1. Open your favorite browser (Chrome, Safari or Firefox as your browser, not Internet Explorer!)
2. Browse to your Galaxy instance
3. On the top pannel go to Login or Register

The Galaxy homepage is divided into three panels:

• Tools on the left
• Viewing panel in the middle
• History of analysis and files on the right

Open image in new tab

The first time you use Galaxy, there will be no files in your history panel.

Copernicus Data Space Ecosystem

Hands-on: Launch the interactive tool

1. Copernicus Data Space Ecosystem with the following parameters:
   • “Do you already have a notebook?”: Start with a fresh notebook
   • “Include data into the environment - optional “: You don’t need anything

2. Click on Run Tool

3. Tip: Open interactive tool

   1. Go to User > Active InteractiveTools
   2. Wait for the Copernicus Data Space Ecosystem to be running (Job Info)
   3. Click on Copernicus Data Space Ecosystem

Hands-on: Navigate the jupyterlab

1. Once you are in the jupyterlab go to :
   • notebooks
   • Then, openeo
   • Open the notebook NDVI_Timeseries.ipynb
2. You can start running your notebook. To do so you can go on the pannel displaying button right above the notebook and click on the workflow-run. Everytime you press this button you can excecute a one by one the cells.
3. In the Setup section when you execute the connection cell you’ll have some actions to conduct.
4. First click ont the link appearing, you’re notebook should look like the following :
5. Once you clicked a new window opens. If you don’t have a copernicus account please create one and follow the instructions given.
6. If you have an account sign in and then press the green YES
7. You’ll be redirected to a page letting you know the connection was a success
8. Now, you can go back on your jupyterlab and execute the rest of the notebook.
9. Once you executed the entire notebook you should have a new folder in the left pannel named ndvi-results go in it.
10. Select the 3 files (timeseries-basic.csv, timeseries-masked.csv, timeseries-smoothed.csv) there and click right, and then copy
11. Then go back to the root of your path and go in the ouputs folder. There you can click right and paste the 3 NDVI files (timeseries-basic.csv, timeseries-masked.csv, timeseries-smoothed.csv).
12. This part is now finished you just have to correctly close this notebook. On the top left click on files and then on Shut down.

Go back on your Galaxy window. After a couple minutes you should see your outputs turning green in your history.

Check that your data are in csv format.

Tip: Check datatype

galaxy-pencil, it should be csv

Tip: Changing the datatype

• Click on the galaxy-pencil pencil icon for the dataset to edit its attributes
• In the central panel, click galaxy-chart-select-data Datatypes tab on the top
• In the galaxy-chart-select-data Assign Datatype, select csv from “New type” dropdown
  • Tip: you can start typing the datatype into the field to filter the dropdown menu
• Click the Save button

Holoviz

Hands-on: Launch Holoviz

1. Holoviz with the following parameters:
   • “Do you already have a notebook?”: Start with a fresh notebook
   • “Include data into the environment - optional “: Select timeseries-basic, timeseries-masked and timeseries-smoothed

2. Click on Run Tool

3. Tip: Open interactive tool

   1. Go to User > Active InteractiveTools
   2. Wait for the Holoviz to be running (Job Info)
   3. Click on Holoviz

4. Once, you are in the jupyterlab go in the the notebooks folder
5. Open a terminal in bash and write the following

   Input: Download the notebook

   wget https://raw.githubusercontent.com/fair-ease/Holoviz/main/Tabular_Datasets_NDVI.ipynb
   

Now that you have your notebook you can just follow the instructions.

Enjoy discovering the rest of the notebook.

Conclusion

The tutorial ends there and with that you have the basis on how to use jupyterlab tools and more particularly the copernicus and holoviz ones.

You've Finished the Tutorial

Please also consider filling out the Feedback Form as well!

Key points

• Manage NDVI data

• Handle jupyterlab tools

Frequently Asked Questions

Useful literature

Further information, including links to documentation and original publications, regarding the tools, analysis techniques and the interpretation of results described in this tutorial can be found here.

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Citing this Tutorial

1. Marie Josse, From NDVI data with OpenEO to time series visualisation with Holoviews (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/tutorial.html Online; accessed TODAY
2. Hiltemann, Saskia, Rasche, Helena et al., 2023 Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 10.1371/journal.pcbi.1010752
3. Batut et al., 2018 Community-Driven Data Analysis Training for Biology Cell Systems 10.1016/j.cels.2018.05.012

BibTeX

@misc{ecology-ndvi_openeo,
author = "Marie Josse",
	title = "From NDVI data with OpenEO to time series visualisation with Holoviews (Galaxy Training Materials)",
	year = "",
	month = "",
	day = "",
	url = "\url{https://training.galaxyproject.org/training-material/topics/ecology/tutorials/ndvi_openeo/tutorial.html}",
	note = "[Online; accessed TODAY]"
}
@article{Hiltemann_2023,
	doi = {10.1371/journal.pcbi.1010752},
	url = {https://doi.org/10.1371%2Fjournal.pcbi.1010752},
	year = 2023,
	month = {jan},
	publisher = {Public Library of Science ({PLoS})},
	volume = {19},
	number = {1},
	pages = {e1010752},
	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
	editor = {Francis Ouellette},
	title = {Galaxy Training: A powerful framework for teaching!},
	journal = {PLoS Comput Biol}
}

                   

Funding

These individuals or organisations provided funding support for the development of this resource

Fair-Ease

FAIR-EASE is a RIA project funded under HORIZON-INFRA-2021-EOSC-01-04, and it involves a consortium of 25 partners from all over Europe.

EuroScienceGateway

EuroScienceGateway was funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963.

Galaxy Administrators: Install the missing tools

You can use Ephemeris's shed-tools install command to install the tools used in this tutorial.

shed-tools install [-g GALAXY] [-a API_KEY] -t <(curl https://training.galaxyproject.org/training-material/api/topics/ecology/tutorials/ndvi_openeo/tutorial.json | jq .admin_install_yaml -r)

Alternatively you can copy and paste the following YAML

---
install_tool_dependencies: true
install_repository_dependencies: true
install_resolver_dependencies: true
tools: []

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