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  • 03:40
    proceps commented #2594
  • 03:36
    mjy commented #2594
  • 03:08
    proceps commented #2594
  • 03:05
    mjy opened #2594
  • 03:05
    mjy labeled #2594
  • Oct 25 20:44
    tmcelrath commented #2593
  • Oct 25 20:42

    proceps on development

    regex date format update (compare)

  • Oct 25 20:42
    tmcelrath opened #2593
  • Oct 25 20:05

    jlpereira on development

    Fix verbatim label (compare)

  • Oct 25 19:51

    jlpereira on development

    Add dataset type (compare)

  • Oct 25 19:38

    jlpereira on development

    Remove classes (compare)

  • Oct 25 19:17
    mjy labeled #2592
  • Oct 25 19:17
    mjy opened #2592
  • Oct 25 19:17
    mjy labeled #2592
  • Oct 25 14:49

    proceps on development

    closes #2590 (compare)

  • Oct 25 14:47
    proceps closed #2590
  • Oct 25 14:47

    proceps on development

    closes #2590 (compare)

  • Oct 25 14:07
    LocoDelAssembly closed #2589
  • Oct 25 14:07

    LocoDelAssembly on development

    Fix #2589: fixed authorship par… (compare)

  • Oct 25 04:40
    mjy opened #2591
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
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
image.png
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
image.png
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
image.png
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
:P
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".