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Various fusion bugfixes #1119

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merged 3 commits into from
Oct 2, 2024
Merged

Various fusion bugfixes #1119

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17f0c39
Comment out any order by LENGTH statements since they cause unexplain…
susannasiebert Oct 1, 2024
2d1066e
Add coordinate stub on gene variant creation
susannasiebert Oct 2, 2024
ff24bc3
actually invoke promise callback for count calculation
acoffman Oct 2, 2024
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12 changes: 6 additions & 6 deletions server/app/graphql/types/queries/typeahead_queries.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -81,13 +81,13 @@ def disease_typeahead(query_term:)
base_query = Disease.where(deprecated: false)
results = base_query.where("diseases.name ILIKE ?", "%#{query_term}%")
.or(base_query.where("diseases.doid ILIKE ?", "#{query_term}%"))
.order("LENGTH(diseases.name) ASC")
#.order("LENGTH(diseases.name) ASC")
.limit(10)
if results.size < 10
secondary_results = base_query.eager_load(:disease_aliases)
.where("disease_aliases.name ILIKE ?", "%#{query_term}%")
.where.not(id: results.select('id'))
.order("LENGTH(diseases.name) ASC")
#.order("LENGTH(diseases.name) ASC")
.distinct
.limit(10-results.size)
return results + secondary_results
Expand All @@ -100,7 +100,7 @@ def therapy_typeahead(query_term:)
base_query = Therapy.where(deprecated: false)
results = base_query.where("therapies.name ILIKE ?", "#{query_term}%")
.or(base_query.where("therapies.ncit_id ILIKE ?", "%#{query_term}%"))
.order("LENGTH(therapies.name) ASC")
#.order("LENGTH(therapies.name) ASC")
.limit(10)
if results.size < 10
secondary_results = base_query.where('therapies.name ILIKE ?', "%#{query_term}%")
Expand All @@ -110,7 +110,7 @@ def therapy_typeahead(query_term:)
tertiary_results = base_query.eager_load(:therapy_aliases)
.where("therapy_aliases.name ILIKE ?", "%#{query_term}%")
.where.not(id: results.select('id') + secondary_results.select('id'))
.order("LENGTH(therapies.name) ASC")
#.order("LENGTH(therapies.name) ASC")
.distinct
.limit(10-results.size)

Expand All @@ -131,14 +131,14 @@ def feature_typeahead(query_term:, feature_type: nil)
end

results = base_query.where('features.name ILIKE ?', "#{query_term}%")
.order("LENGTH(features.name) ASC")
#.order("LENGTH(features.name) ASC")
.limit(10)

if results.size < 10
secondary_results = base_query.eager_load(:feature_aliases)
.where("feature_aliases.name ILIKE ?", "#{query_term}%")
.where.not(id: results.select('id'))
.order("LENGTH(features.name) ASC")
#.order("LENGTH(features.name) ASC")
.distinct
.limit(10 - results.size)
return (results + secondary_results).uniq
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2 changes: 1 addition & 1 deletion server/app/graphql/types/variants/gene_variant_type.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,7 @@ def mane_select_transcript
def open_revision_count
Loaders::AssociationCountLoader.for(object.class, association: :open_revisions).load(object.id).then do |count|
Loaders::AssociationLoader.for(Variants::GeneVariant, :coordinates).load(object).then do |coord|
Loaders::AssociationCountLoader.for(VariantCoordinate, association: :open_revisions).load(coord.id) do |coord_count|
Loaders::AssociationCountLoader.for(VariantCoordinate, association: :open_revisions).load(coord.id).then do |coord_count|
count + coord_count
end
end
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10 changes: 10 additions & 0 deletions server/app/models/activities/create_variant.rb
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,19 @@ def call_actions

@variant = cmd.variant
@molecular_profile = cmd.molecular_profile

stub_coordinates
variant.save!

events << cmd.events
end

def stub_coordinates
if variant.type == 'Variants::GeneVariant'
variant.coordinates = VariantCoordinate.generate_stub(variant, 'Gene Variant Coordinate')
end
end

def linked_entities
molecular_profile
end
Expand Down
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