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add disease_context_qualifier to model and regenerate artifacts #850

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merged 5 commits into from
Oct 17, 2024
+113,967 −109,950
Merged

add disease_context_qualifier to model and regenerate artifacts #850

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7ba3e88
add disease_context_qualifier to model and regenerate artifacts
kevinschaper Oct 15, 2024
16622ba
add closure fields for disease context qualifier
kevinschaper Oct 16, 2024
4a8bc7b
update to linkml 1.8.3, tweak get_entity method to construct the node…
kevinschaper Oct 17, 2024
820a210
update fixtures
kevinschaper Oct 17, 2024
faa58d9
type check fixes
kevinschaper Oct 17, 2024
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type check fixes
@kevinschaper
kevinschaper committed Oct 17, 2024
commit faa58d9b75eeab42ca223163e6dd0cc011ece91c
2 changes: 1 addition & 1 deletion frontend/src/api/phenotype-explorer.ts
View file
Original file line number Diff line number Diff line change
@@ -43,7 +43,7 @@ export const getPhenotypes = async (search = ""): ReturnType<OptionsFunc> => {
* if gene/disease, provide function to get associated phenotypes upon
* select
*/
item.category.startsWith("biolink:Pheno")
item.category?.startsWith("biolink:Pheno")
? undefined
: async () => await getPhenotypeAssociations(item.id),
highlight: item.highlight,
2 changes: 1 addition & 1 deletion frontend/src/pages/explore/TabSearch.vue
View file
Original file line number Diff line number Diff line change
@@ -240,7 +240,7 @@ async function runGetAutocomplete(
viewAll,
...(await getAutocomplete(search)).items.map((item) => ({
id: item.id,
label: item.name,
label: item.name || "",
info: item.in_taxon_label || item.id,
icon: getCategoryIcon(item.category),
tooltip: "",

Unchanged files with check annotations Beta

View file
backend/src/monarch_py/implementations/solr/solr_implementation.py
return parse_entity(solr_document)
# Get extra data (this logic is very tricky to test because of the calls to Solr)
entity = Entity(**solr_document)
entity.uri = get_uri(entity.id)
if "biolink:Disease" == entity.category:

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backend/src/monarch_py/implementations/solr/solr_implementation.py#L96-L98 

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# Get mode of inheritance
mode_of_inheritance_associations = self.get_associations(
subject=id, predicate=[AssociationPredicate.HAS_MODE_OF_INHERITANCE], direct=True, offset=0
)
if mode_of_inheritance_associations is not None and len(mode_of_inheritance_associations.items) == 1:
entity.inheritance = self._get_counterpart_entity(mode_of_inheritance_associations.items[0], entity)

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# Get causal gene
entity.causal_gene = [

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self._get_counterpart_entity(association, entity)
for association in self.get_associations(
object=id,
category=[AssociationCategory.CAUSAL_GENE_TO_DISEASE_ASSOCIATION],
).items
]
if "biolink:Gene" == entity.category:
entity.causes_disease = [

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self._get_counterpart_entity(association, entity)
for association in self.get_associations(
subject=id,
category=[AssociationCategory.CAUSAL_GENE_TO_DISEASE_ASSOCIATION],
).items
]
node: Node = Node(

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**entity.dict(),
node_hierarchy=self._get_node_hierarchy(entity),
association_counts=self.get_association_counts(id).items,