Merge pull request #148 from x-atlas-consortia/jas_fix_sources

Bug fix to sources endpoint
x-atlas-consortia · Aug 12, 2024 · affaf1d · affaf1d
2 parents 27bff22 + 6c94ed5
commit affaf1d
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/ubkg_api/cypher/sources.cypher b/src/ubkg_api/cypher/sources.cypher
@@ -16,7 +16,7 @@ CALL
 CALL
 {
 	WITH CUISource
-	 MATCH (pSource:Concept)-[:has_sab]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
+	MATCH (pSource:Concept)-[:has_sab]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
 	WHERE pSource.CUI=CUISource
 	$sabfilter
 	AND r.CUI = p.CUI
@@ -44,7 +44,7 @@ CALL
 CALL
 {
 	WITH CUISource
-	MATCH (pSource:Concept)-[:has_home_url]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
+	OPTIONAL MATCH (pSource:Concept)-[:has_home_url]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
 	WHERE pSource.CUI=CUISource
 	AND r.CUI = p.CUI
 	RETURN COLLECT(t.name) AS home_urls
@@ -53,7 +53,7 @@ CALL
 CALL
 {
 	WITH CUISource
-	MATCH (pSource:Concept)-[:has_source_dictionary_url]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
+	OPTIONAL MATCH (pSource:Concept)-[:has_source_dictionary_url]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
 	WHERE pSource.CUI=CUISource
 	AND r.CUI = p.CUI
 	RETURN t.name AS source_dictionary_url
@@ -62,7 +62,7 @@ CALL
 CALL
 {
 	WITH CUISource
-	MATCH (pSource:Concept)-[:has_citation]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
+	OPTIONAL MATCH (pSource:Concept)-[:has_citation]->(p:Concept)-[:CODE]->(c:Code)-[r:PT]->(t:Term)
 	WHERE pSource.CUI=CUISource
 	AND r.CUI = p.CUI
 	RETURN COLLECT(DISTINCT {PMID:split(t.name,':')[1], url:'https://pubmed.ncbi.nlm.nih.gov/'+split(t.name,':')[1]}) AS citations

diff --git a/ubkg-api-spec.yaml b/ubkg-api-spec.yaml
@@ -459,7 +459,7 @@ paths:
           description: A sequential set of relationships that specifies the pattern of relationships in the paths in the subgraph. Each element in the set should be in format SAB:relationship type. SAB corresponds to the source in which the relationship was asserted--e.g., "NCI:is_marked_by_gene_product" corresponds to the "is_marked_by_gene_product" relationship asserted in NCI. The set can be specified with a list of values delimited with commas (e.g., ?relsequence=SAB1:relationshiptype1,SAB2:relationshiptype2) or with individual key-value pairs (e.g., ?relsequence=SAB1:relationship_type1&relsequence=SAB2:relationshiptype2).
           schema:
             type: string
-            example: NCI:is_marked_by_gene_product,NCI:3Agene_product_encoded_by_gene
+            example: NCI:is_marked_by_gene_product,NCI:gene_product_encoded_by_gene
         - name: skip
           in: query
           required: false