Argo decoder tool #105
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Argo decoder tool #105
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bgruening
reviewed
Mar 22, 2024
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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@bgruening Is the tool good enough for a 1st try to deploy it or not ? |
bgruening
reviewed
Apr 10, 2024
| <test expect_num_outputs="1"> | ||
| <param name="raw_data" value="data_input_20240319.zip"/> | ||
| <param name="float_wmo" value="6903014"/> | ||
| <output name="outputs_data" value="argo-decoder-outputs.zip"/> |
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what do you think about using https://docs.galaxyproject.org/en/latest/dev/schema.html#assertions-for-archives-zip-tar
To assert certain files in this archive, this would also enable us to remove this file.
bgruening
reviewed
Apr 10, 2024
bgruening
reviewed
Apr 10, 2024
| ]]> | ||
| </command> | ||
| <inputs> | ||
| <param name="raw_data" type="data" format="zip" label="Archived input argo raw data"/> |
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The label is a bit confusing to me. Where is this data coming from? Why is it archived?
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| <citation type="bibtex"> | ||
| @Manual{, | ||
| title = {Coriolis data processing chain for Argo floats}, | ||
| author = {Ifremer}, | ||
| year = {2024}, | ||
| note = {https://github.com/euroargodev/Coriolis-data-processing-chain-for-Argo-floats} | ||
| </citation> |
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Suggested change
| <citation type="bibtex"> | |
| @Manual{, | |
| title = {Coriolis data processing chain for Argo floats}, | |
| author = {Ifremer}, | |
| year = {2024}, | |
| note = {https://github.com/euroargodev/Coriolis-data-processing-chain-for-Argo-floats} | |
| </citation> |
The DOI is maybe enough?
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can we make this smaller?
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
Co-authored-by: Björn Grüning <bjoern@gruenings.eu>
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.shed.yml is missing I think |
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So, this is a batch tool using a docker image as a requirement.
To work properly we will need to add a line there : https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/tpv/interactive_tools.yml#L52 to change the user.
The docker image is heavy so we'll see if it's possible to use it.
The image once build is publicly accessible there ghcr.io/euroargodev/coriolis-data-processing-chain-for-argo-floats:061a-galaxy
For now the docker file is on a private gitlab but will soon be on a public github thanks to @leobr29.
I am starting this PR to see what needs to be improve and see the best ways to make this new tool work. This is a 1st version to make a demo for the Argo community in April. The aim is then to improve the tool (for instance remove all the zip and make more readable inputs and outputs) and create a workflow where we can access the argo data, decode them, and then visualize and analyze them with scoop-argo, ODV and DIVAnd.
I am not sure I'm making the PR in the right place. I put it with the other argo related tool.
Thoughts ?? Comments ??
Plus, I don't know how to make planemo test work (or if it's even possible) with a docker as a dependence