Add ADAM Tool

[annefou]

Add tools for retrieving data from the Advanced geospatial Data Management platform (ADAM).

Under development in adam branch: https://github.com/NordicESMhub/galaxy-tools/tree/adam

• [ ] Add adamapi in conda-forge (only available in pypi: https://pypi.org/project/adamapi/)
• [ ] Adam Info to search for datasets in the ADAM data cubes
• [ ] ADAM retrieve to retrieve selected datasets from ADAM data cubes.
• [ ] Allow users to select the output format (netCDF or GeoTIFF) when retrieving data over a geographical area (when retrieving a single position where tabular is the only available output format).

[Burnleydev1]

Hello @annefou I am an outreachy intern and would like to ask more about this issue, and to know if it is possible for me to attempt it.

[annefou]

Hi @Burnleydev1 That would be very useful for me and I would be happy to provide support and guidance for this task. This is something that could be done for example during the outreachy intership. First, I'd like to make sure that you are aware of the steps we defined for assessing Outreachy interns (see the project detail description and how applicants can contribute):

• Join the Matrix/Element Galaxy-Outreachy chat channel: https://matrix.to/#/#outreachy-climate:matrix.org,  introduce yourself and join in conversations. This is where you can reach project mentors. There might be many applicants interested in the project, please support each other.
• Visit the Galaxy Community Hub (https://galaxyproject.org/) to get familiar with Galaxy and its community. Complete one of these introductory tutorials (https://training.galaxyproject.org/training-material/topics/introduction/) on Galaxy Europe instances (https://usegalaxy.eu/ or https://climate.usegalaxy.eu/) and record your first contribution in the Outreachy site adding a link to your public history.

1. Galaxy 101 for everyone
2. A short introduction to Galaxy
3. Introduction to Genomics and Galaxy
4. How to reproduce published Galaxy analysis
5. From peaks to genes
6. Galaxy 101

• Watch the Galaxy Climate “Introduction to climate data” and complete one of these Galaxy Climate tutorials (https://training.galaxyproject.org/training-material/topics/climate/) on Galaxy Europe instance (https://usegalaxy.eu/ or https://climate.usegalaxy.eu/) and record your second contribution in the Outreachy site adding a link to your public history.

  1. Getting your hands-on climate data
  2. Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools
  3. Functionally Assembled Terrestrial Ecosystem Simulator (FATES)

• Using Open data from ECMWF ERA5 Reanalysis, create your own plots/maps with Xarray Galaxy Tools and record your third contribution in the Outreachy site adding a link to your public history containing:

  1. A global map of air temperature at 2 meters for the last available day on Galaxy Europe (Upload Data → Choose remote files → ECMWF ERA5 Reanalysis)
  2. A regional map (for the same variable and date) over your own country (to simplify, you can select a geographical rectangular area that includes your country of residence)
  3. A tabular file containing a single row with the air temperature at 2 meters (extracted from the same input file as above) for the location that is closest to where you live.

• Create a Github repository that publishes/displays the results of your Galaxy history (two plots of air temperature at 2 meters on global and regional maps and value of air temperature at 2 meters at a given location e.g. closest point where you live) on github gh-pages. You may use the Galaxy Training material “Automating Galaxy workflows using the command line” from the Galaxy training on “Using Galaxy and Managing your Data”.

• Write a blog post describing all the regional/local initiatives you know about, if any exists, or what you would like to see/do and how Galaxy Climate cloud could support their combat against climate change in the region/city/place you live in. In particular, highlight what is currently done locally, or what could be done to monitor energy/water usage (including recycling and waste conversion) and greenhouse gasses emissions (but also CO2 capture, reforestation, etc.), run analysis, and identify strategies to reduce waste and emissions e.g. to create the foundations for effective climate actions. Publish it online in a platform of your choice and record your contribution in the Outreachy site.

• Post about your experience on Social Media and record your contribution in the Outreachy site.