Upload season 7 leaf chemistry data

[dlebauer]

Need to upload data from Duke Pauli from Oct 8. See forwarded email for data.

• [x] put spreadsheets from email on google drive
• [x] create a worksheet of variables in a worksheet
  • some will already exist, many dont
  • only need 'dry basis'
  • [x] identify any duplicate variables, and keep a list of these
  • [x] identify variables that combine the trait and the method, and define new methods as necessary (e.g. crude_protein with harvestlab vs ward labs should be distinguisted by the method, not the variable name)
• [x] define a new method that relates to the NIR feed analyses from Ward Laboratories
• [x] use the sampleID to combine results data (csv file) with plot names
• [x] review the documentation for uploading traits via BETYdb API, and prepare a csv to be uploaded
• [x] add sample date = oct 8 2018

[dlebauer]

For the existing crude_protein and sugar content variables, we need to distinguish the variable from the method. These data were measured using the John Deer Harvestlab 3000 https://www.deere.com/en/technology-products/precision-ag-technology/data-management/harvest-lab-constituent-sensing/

Prior to uploading the new leaf chemistry data, please:

• [x] create a new method and citation that describes the HarvestLab and the fact that it is measured on stem + leaf.
• [x] Update the variable descriptions to remove the reference to the harvestlab method
• [x] update the existing trait records of crude_protein and sugar_content to link the harvestlab method

[kimberlyh66]

The trait records for crude_protein and sugar_content are already linked to a citation. Will there be a problem if I update the method for the records to be harvestlab which is linked to a new citation?

[dlebauer]

@kimberlyh66 no - the trait data is linked to one citation record that identifies the person or publication responsible for the data (in this case, Duke Pauli) while the method record is linked to a citation that describes the method of measurement - in this case there will be one method with a citation pointing to HarvestLab documentation and the other method to documentation from Ward Laboratories.

[kimberlyh66]

@dlebauer thanks for the clarification. Here is the update statement to link the existing trait records of crude_protein and Sugar_content to the new harvestlab method.

update traits
set method_id = (select id from methods where name = 'Protein leaf and stem measurement')
where variable_id in ((select id from variables where name = 'crude_protein'), (select id from variables where name = 'Sugar_content'));

Also, I have temporarily assigned the year to be 2019 in the new harvestlab citation. Do you know what the year should be?

[dlebauer]

thanks. If you are referencing a website, use the access date of 2019. If a pdf, either use the publication date or the access date.

[dlebauer]

I've updated the protein methods in the database per https://github.com/terraref/reference-data/issues/258#issuecomment-453586661

[kimberlyh66]

Sites with data need to be associated with Duke Pauli's citation. Here is the insert statement.

insert into citations_sites (citation_id, site_id)
  select c.id, s.id
  from (select id from citations where author = 'Duke Pauli')
    as c cross join (select id from sites where sitename ~ '^MAC Field Scanner Season 7 ((Range (17|18|19|20|21|22|23|24|26|27|28) Column (2|3|4|5|6|7|8|9|10|11|12|13|14|15))|(Range 25 Column (2|3|4|6|7|8|9|10|11|12|13|14|15)))$') as s;

It looks like there is no data for Range 25 Column 5.

[dlebauer]

this has been completed