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New fields for Batches entity #1863
New fields for Batches entity #1863
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@leandroradusky could you briefly explain what those fields are about? |
I will do it in the main text of the issue when we have the full details... But as an advance: these two mentioned above are names that the viruses within the batches have in global reference databases: |
Shall the fields be free text, or would we like to have a database of all these names? The former is prone to human typos, while the second means we must keep the databases updated, which we probably don't want to. |
@leandroradusky what do you say if we make these fields dropdowns/autocomplete? Plus an "other" option for entering the value manually if not found? |
This can be done, we should confirm with them where they get this labels for different DBs and analyze if we can have a table, or if we should be constantly updating them from online resources (taxonomy id, I believe, will update each time there is a new strain of covid or whatever other organism, and they will need to add the options "constantly"─there isn't now one new strain per week, but in the peak of covide there were). |
Just a note that the estimation will be completely different: syncing a local copy of a database is more complex than having free text inputs. |
The conclusion regarding the fields to be free text or combos, is described in the section |
@diegoliberman still need some clarification
If no values have been previously entered in these fields for batches from the same institution, the autocomplete feature will not have any suggestions to offer. Conversely, if there have been values entered in these fields for past batches from the same institution, the autocomplete feature will provide these as suggestions when inputting data into these fields. Thats correct?
(reference_gene, target_organism_taxonomy_id, pango_lineage, who_label) this new field should be also in Sample model?
For example, if you have a Batch with a reference_gene of "N", and later you are entering a Sample, "N" should come up as a suggestion for the reference_gene in the Sample as well, and vice versa. that's correct? |
@bolom the answer for the 3 questions is --> correct :) |
* Fix BachForm to use correct name Fix Lint Syntax Issue Update autocomplete.js.jsx * AutoComplete Feature for Batch Model * Delete autocomplete.js.jsx Update batches_controller.rb Delete autocomplete_value.rb Update batch_form.rb Update institution.rb remove unused files Update _form.haml * Add react component helper: autocomplete_field * Optimize Loading Values * Fix test Suite Fix TextSuite * Fix: add combobox props to CdxSelectAutocomplete to fix broken autocomplete to box form * Fix: debounce calls to CdxSelectAutocomplete to reduce stress on server * Use Send instead of try in unique_values_for --------- Co-authored-by: Julien Portalier <julien@portalier.com>
@bolom It is working fine. |
The
Batch
entity within CDx is missing some data to be complete in regard to the data that needs to be uploaded to NIH.These new columns need to be added to batches:
copies
of the virus (i.e.concentration
where its units iscopies/ml
) but what this count on reality is not copies of the virus, but based on a reference gene that can be counted experimentally. This depends on the methods used, in our scenario will be almost always equal toN
the nucleocapsid protein but this, for other organisms could be whatever gene.Field labels:
All of them are combo free text fields:
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