4409 y24 379 study setup fields to align to the ena database fields #4542
Conversation
| @@ -286,6 +295,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength | |||
| allow_blank: true | |||
| } | |||
|
|
|||
| validates :ebi_library_strategy, inclusion: { in: EBI_LIBRARY_STRATEGY_OPTIONS } | |||
There was a problem hiding this comment.
Can these be nil or are these required for all studies? Do we need to add a conditional to these so they are just checked for ENA studies?
There was a problem hiding this comment.
the story states cannot be empty.
| @@ -31,7 +31,10 @@ def create_study | |||
| contaminated_human_dna: 'No', | |||
| contains_human_dna: 'No', | |||
| commercially_available: 'No', | |||
| program: UatActions::StaticRecords.program | |||
| program: UatActions::StaticRecords.program, | |||
| ebi_library_strategy: 'WGS', | |||
There was a problem hiding this comment.
Do these need to be here, are they mandatory for all studies?
| @@ -14,6 +14,10 @@ | |||
| <%= group.plain_value(:study_sra_hold) %> | |||
| <% end %> | |||
|
|
|||
| <%= metadata_fields.plain_value(:ebi_library_strategy) %> | |||
There was a problem hiding this comment.
Should these be part of the above ENA requirement group?
db/migrate/20241126115246_add_ebi_library_strategy_to_studay_metadata.rb
Outdated
Show resolved
Hide resolved
| @@ -0,0 +1,9 @@ | |||
| # frozen_string_literal: true | |||
|
|
|||
| file_path = Rails.root.join('config/ena_requirement_fields.yml') | |||
There was a problem hiding this comment.
It is looking for ena_requirement_fields but the file name is ENA_requirement_fields.
It is probably better to use config_for rather than an initializer.
| @@ -90,6 +90,10 @@ class Study < ApplicationRecord # rubocop:todo Metrics/ClassLength | |||
|
|
|||
| DATA_RELEASE_DELAY_PERIODS = ['3 months', '6 months', '9 months', '12 months', '18 months'].freeze | |||
|
|
|||
| EBI_LIBRARY_STRATEGY_OPTIONS = EBI_REQUIREMENT_FIELDS['EBI_Library_strategy'] | |||
There was a problem hiding this comment.
If you use config_for then you can use the options directly in study without having to redefine them.
Closes #
Changes proposed in this pull request
Add EBI:Library Strategy as field with a combobox of options from here to the Study Setup page. This must be selected and cannot be left empty.
Add EBI: Library Source, as field with a combobox of options from here to the Study Setup page. This must be selected and cannot be left empty.
Add EBI:Library Selection, as field with a combobox of options from here to the Study Setup page. This must be selected and cannot be left empty.
Export these additional fields to the MLWH.
Remove the "ENA requirement" text from the Study Type field on Study Setup page.
Add the "ENA requirement" text to the EBI:Library Strategy, EBI: Library Source and EBI:Library Selection fields.
Instructions for Reviewers
[All PRs] - Confirm PR template filled
[Feature Branches] - Review code
[Production Merges to
main]- Check story numbers included
- Check for debug code
- Check version