Unexpected results and invalid EML with "expand_taxa=FALSE" in create_EML

[gremau]

I recently updated MetaEgress and updated my workflow to use the "expand_taxa" and "skip_taxa" arguments to the create_EML function. When I set "expand_taxa=TRUE" my taxa are expanded into a nice tree in the resulting EML. When I set "expand_taxa=FALSE" an invalid EML document is produced. No taxa expansion happens (as expected), but there are some elements in the resulting <taxonomicClassification> element that won't validate (I think <commonname> is the problem but not sure). One good thing about "expand_taxa=FALSE" is that there is a <taxonId> element with the provider="https://itis.gov" attribute. This element does not appear with "expand_taxa=TRUE" as I was originally expecting.

It seems that "expand_taxa=FALSE" should still give valid EML with a taxonomicCoverage element, but I'm not sure where things are going wrong. Let me know if anyone has thoughts on how to correct this. 2 EML documents are attached (=FALSE and =TRUE cases)

knb-lter-jrn.210121001.62_expandfalse.xml.txt

knb-lter-jrn.210121001.62_expandtrue.xml.txt

[twhiteaker]

Did your parser tell you why the EML was invalid?

Without An, we've lost a lot of expertise to debug R stuff at BLE.

[twhiteaker]

One issue is that commonname should be commonName.
https://github.com/NCEAS/eml/blob/main/xsd/eml-coverage.xsd#L1119

It's also weird that commonname appears in the expand=false version but not the expand=true version.

Another issue is that the rank name and value should occur before the common name and taxonId, I think, since this is an xs:sequence.
https://github.com/NCEAS/eml/blob/main/xsd/eml-coverage.xsd#L1086

[gremau]

When validating the "expand_taxa=FALSE" file the first error I get is

"Error at line 217, column 23: no declaration found for element 'commonname'"

I then tried replacing commonname with commonName (camelcase) and got a different error:

"Error at line 221, column 35: element 'taxonRankName' is not allowed for content model '(taxonRankName?,taxonRankValue?,commonName*,taxonId*,taxonomicClassification*)'"

Bummer about An leaving BLE! She was great, and I hope we can keep MetaEgress and other projects going in her absence.

[gremau]

Good catch. At some point I can try to debug (might not be today though) - it seems like there is probably a logic issue and elements need to be reordered in the R code to satisfy the schema, but I'm not totally clear where to find that yet.

[twhiteaker]

Oh, it was also strange to me that commonName didn't show up in your expanded version. Common name does appear in the expanded versions that An generated for BLE.

[twhiteaker]

I think commonname in line 179 of assemble_taxonomy.R needs to be commonName.
As for rank name and value being out of order, I don't know yet.

[twhiteaker]

In 583a746, I fix the spelling to commonName. I exported EML with the expand_taxa option to set True and again set to False. Both outputs validated using this parser.

However, I don't see any common names in the output.

[twhiteaker]

For expand_taxa =FALSE, MetaEgress reads from Metabase. All my common names were empty. Once I entered a common name, it showed up in EML.

For expand_taxa =TRUE, I assume MetaEgress calls something like taxize to pull the info. WoRMS doesn't return common names as far as I can tell, and all of my datasets use WoRMS. @gremau do you have a dataset that uses some other provider that does provide common names, that you can test with?