Boku

[MarkusKonk]

This is a template to structure the integration of the use cases' analyses into AquaINFRA's virtual research environment.
Please copy this template and assign all those who should be involved using the "Assignees" - feature on the right, for example, any developers or use case members from your side.

And please use the comment section below. No mailing will be necessary and the entire communication is in one place. Individual persons can be pinged using, for instance, @MarkusKonk

Description

• Rather a technical than a thematic description
• How to run the analysis?
• Which programming languages are used?
• How does the workflow look like?
• Which functions are used and how are they connected?
• Anything else needed to run the analysis?

URLs

URL to input datasets: Different ones for each process, to be provided by user.
URL to GitHub: https://github.com/AnthonyBasooma/specleanr/blob/aquabranch/

Commands for running R/Python scripts

https://github.com/AnthonyBasooma/specleanr/blob/aquabranch/src/README.md

Commands for running Docker commands:

https://github.com/AnthonyBasooma/specleanr/blob/aquabranch/src/README.md

cURL Commands for running OGC API Processes:

https://github.com/AnthonyBasooma/specleanr/blob/aquabranch/src/README.md

Checklist

• Input data is identified and/or accessible via DDAS
  • Input data is made accessible under an open license
• Analysis code is available on GitHub
  • Analysis code is made accessible under an open license
• Workflow is sketched
• Analysis is split into reusable functions
  • Input parameters are identified
  • functions follow input - processing - output - logic
  • input data can be passes via URL
  • output data is stored in file, e.g., csv, json etc.
• Reusable functions are saved in separate files
• Runtime, libraries, and library versions identified
• R commands are added to README
• Analysis is dockerized
• Docker commands are added to README
• OGC API Processes created locally
  • python scripts created
  • titles and descriptions for input parameters added to json
• OGC API Processes deployed on server
• Tests successful
• Galaxy tool created locally
• Galaxy tool deployed on server
• Tests successful
• Workflow is complete

Detailed To do list for Berlin Stay

• Merret to update matchdata so that users can send EITHER species names, OR a CSV and a column name. (Note: I pushed this, but it is not on the server yet - to do Monday).
• Merret to update matchdata so that user can send a list of n datasets!
• Anthony to update the non-nested parameters, for us to review on Monday (add multidetect to that, as we will not nest them!)
• (Anthony, optional: Review the names of the processes like the URL - now it is still easy to change! Once it is on Galaxy, it gets harder.)
• (Anthony, optional: Review the "granularity" of the processes! Those five are just MY suggestion based on the vignette - you are free to combine them, or slice them to pieces... Or provide two multidetect depending on whether it is one species or several... Up to you)
• Anthony: Come up with a list of more function/tools/processes for specleanr, if you want!
• Anthony: Look at fwtraits! Which functions/tools/processes you want? Already try to write those run scripts (in /src/...R) for that... Or at least come up with the desires inputs.

[MarkusKonk]

What happens if a particular parameter like kmpar =list(k=6, method='silhouette', mode='soft'), which has nested inputs?

@AnthonyBasooma @merretbuurman

how about asking users to pass separate input parameters?
Then you would have something like:

input_k = args[1]
input_method = args[2]
input_mode = args[3]

kmpar =list(k=input_k, method=input_method, mode=input_mode)

Then you could also think of pre-defining possible input values if possible. Based on this, we can create things like dropdown menus or sliders.

[AnthonyBasooma]

@MarkusKonk @merretbuurman I have defined them that way, and so far, the arguments are 49. Hopefully, it works.

[MarkusKonk]

49? What do you mean?
Have you thought of pre-defining the input values?

[AnthonyBasooma]

I have finished the script source for multidetect. I wanted to share it here, but it's not possible. @MarkusKonk @merretbuurman . I have provided a list of default parameters that can be set without breaking the code.

[AnthonyBasooma]

I think I have finally forked the AquaINFRA/spcleanr/aquabranch by Merret.
I am making changes in this
https://github.com/AnthonyBasooma/aquaboku/tree/aquabranchforked @merretbuurman. Can you get the chnages?

[AnthonyBasooma]

I think I have finally forked the AquaINFRA/spcleanr/aquabranch by Merret.
https://github.com/AnthonyBasooma/aquaboku/tree/aquabranchforked @merretbuurman @MarkusKonk
Does this option works?

[merretbuurman]

Hi @AnthonyBasooma , I'm busy this week urgent IGB stuff, I'll be able to look into this next week.

[AnthonyBasooma]

Hello