In LinkML branch: determine section membership with slot group

[turbomam]

preferably as an option, in addition to the current use of is_a parents

slot_group definition

Sujay and I will work on this

This is probably the entry point in main_linkml.js

[turbomam]

Also to do: order the columns by rank

how are they ordered now @ddooley ? By order of appearance in schema.js?

[turbomam]

bump: the linkml datastructure branch does group according to slot_groups now :-) , but it doesn't yet order either sections or columns according to rank.

@sujaypatil96 , you can help with this, right? :-)

[ddooley]

Ordering of DH columns is now by rank on both server side (via linkml.py) and browser side (via script/dataharmonizer/index.js).

[turbomam]

I think the slot_groups have ranks as well. I'll dig something up now.

[ddooley]

As noted on Slack, I missed that “dh_section” is a slot, and under that we have various slot “sub-class” entities, which are referenced by slots’ “slot_group” field. I’ll revise section sorting code to take that into account now.

[turbomam]

The slot analysis_type appears in every enviroment-based template with the title "analysis/data type"

It should appear in column 1 of the sample_id section, which has the title "Sample ID".

I think that's all fine in the linkml-datastructure branch now.

Additionally, sample_id has rank = 1, so it should be the first section

I should implement something that ensures that ranks aren't re-used (like multiple sections with rank = 1)

analysis_type:
  name: analysis_type
  rank: 1
  description: Select all the data types associated or available for this biosample
  title: analysis/data type
  examples:
  - value: metagenomics; metabolomics; proteomics
  see_also:
  - MIxS:investigation_type
  multivalued: true
  slot_group: sample_id
  range: analysis_type_enum
  required: true

---

sample_id:
  name: sample_id
  rank: 1
  title: Sample ID
  from_schema: https://example.com/nmdc_dh
  is_a: dh_section

[ddooley]

The latest push should fix this. For sort, I just had to add a call to fetch slot_group specs from overall specification in order to get rank.

[turbomam]

Yes, section and column layout looks great now.

Did you say you thought that column jumping would be restored in this push? I tried once in my usual setup and it didn't work for me yet.

[turbomam]

Show section isn't working under my use conditions in Chrome, either.

I have seen the jump and show functionality working in FF, but I have also been able to break it by loading data and validating

[ddooley]

There's some odd behaviour with slots that are a subclass of one section but have "slot_group" some other section. Fields in "MIxS core" seems to be problematic this way re. show section, and jumping to them. Looking into it.

[turbomam]

There's some odd behaviour with slots that are a subclass of one section but have "slot_group" some other section

Oh! I don't I intended that to happen. I will look into that later today.

[ddooley]

Not your problem. It turns out menu wasn't refreshing list of template sections or jump to fields. Fixed but have to fix something else before pushing commit on that.

[ddooley]

This should be fixed with latest commit. I didn't catch it earlier because I wasn't doing template change when testing the show/jump functionality.

[turbomam]

Show/jump operations work in Chrome and Firefox

• with the initially opened template
• with a subsequent manually opened template
• after some data has been loaded
• but not after the validation button had been clicked

[ddooley]

K. likely validation causing javascript error that is knocking out other js functions. I will test on your sample data.

[turbomam]

I think this is done. @sujaypatil96 may have some ideas for removing some section arrangement functionality that's replicated between the python can javascript components, but that could be another issue.