SpeciesFileGroup/taxonworks

Workbench for biodiversity informatics.

Hernán Lucas Pereira

@LocoDelAssembly

2.7.4 :002 > ap CollectionObject
class CollectionObject < ApplicationRecord {
                           :id => :integer,
                        :total => :integer, # Allowed in importer
                         :type => :string,
                   :created_at => :datetime,
                   :updated_at => :datetime,
          :preparation_type_id => :integer,
                :repository_id => :integer,
                :created_by_id => :integer,
                :updated_by_id => :integer,
                   :project_id => :integer,
    :buffered_collecting_event => :text, # Allowed in importer
      :buffered_determinations => :text, # Allowed in importer
        :buffered_other_labels => :text, # Allowed in importer
       :ranged_lot_category_id => :integer,
          :collecting_event_id => :integer,
               :accessioned_at => :date,
           :deaccession_reason => :string,
             :deaccessioned_at => :date
}
 => nil

Matt

@mjy

I agree @LocoDelAssembly. We need to adjust the interface correspondingly.

Once documentation comes out we'll also eliminate some issues @tmcelrath .

Tommy McElrath

@tmcelrath

True

How do I get lifeStage to import again? Does my Biocuration have to be named “lifeStage”?

Tommy McElrath

@tmcelrath

Hmm, tried that, didn’t work. What’s the SOP for impoirting Biocuration data again? It works for “Sex” in my dataset but not lifeStage for some reason, dataset below

Montelongo_tcm_try_7.tsv

Hernán Lucas Pereira

@LocoDelAssembly

lifeStage DwC term is not supported, but an alternative is provided: https://github.com/SpeciesFileGroup/taxonworks/issues/2424#issue-972064262

(TW:BiocurationGroup:lifestage or any other group, the last part can be name or URI)

Tommy McElrath

@tmcelrath

Got it, thanks. That helps

Matt

@mjy

The "new" image preview/download options are nice @jlpereira, make snagging images out of the filter very easy.

José Luis Pereira

@jlpereira

yah

Tommy McElrath

@tmcelrath

First DWCA upload to Production (16 COs) here we go! [crosses fingers]

Hernán Lucas Pereira

@LocoDelAssembly

Remember you can import single rows to risk it even less ;)

Tommy McElrath

@tmcelrath

Boom!

Looks great!

Matt

@mjy

Heyhey! Now I can reference this in the talk. Thanks for teasing everything out everyone.

Hernán Lucas Pereira

@LocoDelAssembly

Would this be first import ever in production?

Matt

@mjy

Unless Sergei beat him to it.

Tommy McElrath

@tmcelrath

Shoot - was “locality” supposed to go to “verbatimLocality” in Collecting Event?

Because it did not

Hernán Lucas Pereira

@LocoDelAssembly

verbatimLocality is mapped to CollectingEvent.verbatim_locality. locality is not supported.

Tommy McElrath

@tmcelrath

Ah, there’s the rub/

Well - at least it’s only 16 records vs. 2000+

Hernán Lucas Pereira

@LocoDelAssembly

Tommy McElrath

@tmcelrath

yup, makes sense

Hernán Lucas Pereira

@LocoDelAssembly

Although not sure correct mapping for locality or if I should in fact use it in place of current mapping for verbatimLocality

Tommy McElrath

@tmcelrath

weirdly actually - in this case it was actually imported “correctly” because the labels themselves have no “verbatimLocality” but the data dump they provided me does?

Hernán Lucas Pereira

@LocoDelAssembly

locality doesn't look feasible to be mapped into geographic area if the text is supposed to be like in the example.

Tommy McElrath

@tmcelrath

I agree

I just missed it in this particular import

Matt

@mjy

We definitely need the top 5 gotchas

things like this

eventID required for unique CEs, etc.

Highlighting unsupported fields will also be key.

Tommy McElrath

@tmcelrath

Oh that would be great

Basically - “We read this as a column, but it won’t “go anywhere”"

Matt

@mjy

Then

"You can make it go somewhere if you treat it as a data attribute"

Hernán Lucas Pereira

@LocoDelAssembly

Correct, if your project has Predicates and custom attributes enabled with DwC-like URIs the importer will automatically insert them as data attributes for CollectingEvent and/or CollectionObject.

Tommy McElrath

@tmcelrath

Verbatim is misspelled in “new namespace task"

José Luis Pereira

@jlpereira

fixing

Matt

@mjy

Already fixed

on graph branch

José Luis Pereira

@jlpereira

meh, i pushed a fix on dev

Tommy McElrath

@tmcelrath

Is there any way to add documentation to a large number of COs quickly? E.g. I want to add a deed of gift document to a bunch of specimens from a specific accession

Matt

@mjy

@tmcelrath No. We discussed this workflow with Heidi re better tag options. Concept is to tag a set, then apply something to that set. Tag set/building improvements are understood. We could make a one-off task to do this pretty quickly if needed, it's just "Document all specimens in this tag set".

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