Develop basic script to create RO-Crates from B2Share

[juliancervos]

Hi @stopopol, could you upload the script you wrote on B2Share to RO-Crate to this repo? Then we can continue the discussion and development here.

Background info

During a previous grassland pDT meeting, @stopopol proposed some ideas about uploading the data for the pDT to B2SHARE, and also how we could connect this with FDO and integrate with BioDT. Because LTER has a domain there, the metadata could be automatically harvested and we could add some metadata management to filter through BioDT and its pDTs, and similar ideas. For more info on this and the first steps we took, see the meeting page in the wiki.

[stopopol]

Sorry, forgot to link the file: https://github.com/BioDT/biodt-fair/blob/main/pdt_grassland/rocrates_from_b2share.py

[juliancervos]

No problem! I had a look and changed some things (see 336501e on the b2share_script branch). In particular, there are a couple of things about which I'd like to know what you think:

• Moved crate = ROCrate() to the loop to store each record as in a separate RO-Crate directory (as separate datasets). Is that change okay, or did you want to keep all records under a single collection RO-Crate?
• Following your suggestion in a past WP5 meeting, I've been looking into adding a property to specify which RI the dataset comes from. Some existing properties in Schema.org that could be fitting for that are sourceOrganization, producer publisher. For now, I added eLTER as the publisher of the datasets, but which one do you think that fits best?
• I introduced a quick fix for datasets with the / character in its name. For example: "Grassland Dynamics - Matschertal/Val Mazia (Italy) - 2009-2010" would result in an RO-Crate root directory called "Grassland Dynamics - Matschertal" which would contain another nested directory named "Val Mazia (Italy) - 2009-2010".
  • So instead, with crate.write(crate.name.replace('/', '-')) the forward slash is converted to a dash before writing (the name is still unchanged in the metadata).
  • Not sure how frequent / characters are in site names, but there are other options to handle this. For example, using the suffix of the PID to name the directory, or the DEMIS ID and a timestamp, etc.

Let me know what you think @stopopol !

[stopopol]

Hi,

• I'm completely ok with having separate RO-Crate directories
• "publisher" seems like the most fitting option in the case of eLTER
• the quick fix is perfectly fine. slashes are not commonly used in site names but it might occur every now and then.