Address concerns regarding species problems in the app species list report

[andrewvanbreda]

Raising this issue to address some concerns you raised as part of the report I wrote for

https://github.com/NERC-CEH/npms-app/issues/78

I have had a quick look at this.

My conclusions are:

1. The counting issue still needs investigating further by me, but is definetely wrong in the report. It may relate to point two.
2. The problems you raised about the synonyms/common names relate to the structure of the UK Master List and my report is actually returning data in the way I personally intended it to.

For example, Juncus inflexus/effusus/conglomeratus

https://warehouse1.indicia.org.uk/index.php/taxa_taxon_list/edit/368690

It is not listing as having any common names or synonyms, so it won't display a Default Common Name without an item in that box.

My report is also returning Hard Rush / Soft Rush / Compact Rush as a syononym

https://warehouse1.indicia.org.uk/index.php/taxa_taxon_list/edit/636062

This has the same organism key and meaning.

But there are some oddities here,

1. I don't understand why this doesn't appear as a synonym on the Juncus inflexus/effusus/conglomeratus page

2. Hard Rush / Soft Rush / Compact Rush is marked as Latin, so this means it is appearing in the synonyms box on my report even though it isn't latin. I think it is also causing it to display as a synonym of itself on the Warehouse.

I am sure the other problems you noticed are similar.

I have noticed a couple of improvement that could still be made to my report that don't relate to this

1. Currently the frequency count include training data also (whether there is enough of this to affect the ordering I don't know)

2. My report doesn't take into account the Allow Data Entry flag, I could add that if you really wanted. It probably should.....although I am weary at some point we have to say the report is done. I think I best add this?

[sacrevert]

Regarding the two suggestions for improvements in the report:

Currently the frequency count include training data also (whether there is enough of this to affect the ordering I don't know) My report doesn't take into account the Allow Data Entry flag, I could add that if you really wanted. It probably should.....although I am weary at some point we have to say the report is done. I think I best add this?

I don't think either of these is necessary. As I said in the other issue, I think we can consider this report done for Karolis' purposes (accepting that we are not going to be able to fix UKSI issues in a timely fashion)

[sacrevert]

Regarding UKSI oddities, I don't know whether the recent UKSI update has been fully implemented or not. I don't really understand how it is imported into indicia, but, this entry in the Sandbox suggests that the English name for Hard/Soft/Compact Rush is now tagged as vernacular. Whether this version has been imported, and whether it should have resulted in a common name listing under the scientific name entry in the warehouse, I do not know. Perhaps @andrewvanbreda you can check this with John?

I tend towards assuming that the recent UKSI update to indicia is either not complete, or hasn't been implemented properly, because AFAIK @Sam-Amy submitted additional changes to Chris Raper including common names for genus level stuff (e.g. this was edited 29th April 2024: https://uksi-sandbox.nhm.ac.uk/taxon.php?linkKey=NHMSYS0021762125), but these don't appear to be showing in indicia either.

(actually, that example Cochlearia is missing from the 2015 indicator list now for some reason! Which I also don't understand: https://warehouse1.indicia.org.uk/index.php/taxon_list/edit/168

When you have sorted out the organism key issues, if you could send the links to the species list on the warehouse, then I will do a complete check to make sure nothing has dropped off.