Add edge type filtering to DJORNL queries

spec/datasets/djornl/definitions.yaml

@@ -1,4 +1,4 @@
-"$schema": "http://json-schema.org/draft-07/schema#"
+$schema: "http://json-schema.org/draft-07/schema#"
 name: definitions
 title: DJORNL schema definitions
 description: Node and edge metadata definitions for the Dan Jacobson Exascale dataset

spec/datasets/djornl/edge_types_filter.yaml

@@ -0,0 +1,9 @@
+$schema: "http://json-schema.org/draft-07/schema#"
+name: edge_types_filter
+title: Edge Types
+description: Edge types to filter on
+type: array
+items:
+  $ref: "edge_type.yaml"
+default: []
+examples: [['AraNetv2-HT_high-throughput-ppi', 'AraNetv2-LC_lit-curated-ppi'], ['AraGWAS-Phenotype_Associations']]

spec/datasets/djornl/node_type.yaml

@@ -1,4 +1,4 @@
-"$schema": "http://json-schema.org/draft-07/schema#"
+$schema: "http://json-schema.org/draft-07/schema#"
 name: node_type
 title: Node Type
 description: Node types in Dan Jacobson Exascale dataset

spec/stored_queries/djornl/djornl_fetch_all.yaml

@@ -5,21 +5,15 @@ params:
   additionalProperties: false
   properties:
     edge_types:
-      type: array
-      title: Edge types
-      description: Permitted edge types
-      items:
-        $ref: "../../datasets/djornl/edge_type.yaml"
-      default: []
-      examples: [['AraNetv2-HT_high-throughput-ppi', 'AraNetv2-LC_lit-curated-ppi'],['AraGWAS-Phenotype_Associations']]
+      $ref: "../../datasets/djornl/edge_types_filter.yaml"
 query: |
   LET nodes = (
     FOR v IN djornl_node
       RETURN v
   )
   LET edges = (
     FOR e IN djornl_edge
-      FILTER length(@edge_types) > 0 && e.edge_type IN @edge_types || length(@edge_types) == 0
+      FILTER length(@edge_types) == 0 || e.edge_type IN @edge_types
       RETURN e
   )
   RETURN {nodes, edges}

spec/stored_queries/djornl/djornl_fetch_clusters.yaml

@@ -15,17 +15,21 @@ params:
       examples: [['markov_i2:5', 'markov_i6:2'],['markov_i6:1']]
     distance:
       $ref: "../../datasets/distance.yaml"
+    edge_types:
+      $ref: "../../datasets/djornl/edge_types_filter.yaml"
 query: |
   LET node_ids = (
     FOR n IN djornl_node
       FILTER n.clusters ANY IN @cluster_ids
-      FOR node IN 0..@distance ANY n djornl_edge
+      FOR v, e, p IN 0..@distance ANY n djornl_edge
         OPTIONS {bfs: true, uniqueVertices: "global"}
-        RETURN DISTINCT node._id
+        FILTER length(@edge_types) == 0 || p.edges[*].edge_type ALL IN @edge_types
+        RETURN DISTINCT v._id
   )
   LET edges = (
     FOR edge IN djornl_edge
       FILTER edge._from IN node_ids AND edge._to IN node_ids
+        AND (length(@edge_types) == 0 || edge.edge_type IN @edge_types)
       RETURN edge
   )
   LET nodes = (

spec/stored_queries/djornl/djornl_fetch_genes.yaml

@@ -14,17 +14,21 @@ params:
       examples: [["AT1G01010"],["AT1G01020","AT1G01070"]]
     distance:
       $ref: "../../datasets/distance.yaml"
+    edge_types:
+      $ref: "../../datasets/djornl/edge_types_filter.yaml"
 query: |
   LET node_ids = (
     FOR n IN djornl_node
       FILTER n._key IN @keys AND n.node_type == 'gene'
-      FOR node IN 0..@distance ANY n djornl_edge
+      FOR v, e, p IN 0..@distance ANY n djornl_edge
         OPTIONS {bfs: true, uniqueVertices: "global"}
-        RETURN DISTINCT node._id
+        FILTER length(@edge_types) == 0 || p.edges[*].edge_type ALL IN @edge_types
+        RETURN DISTINCT v._id
   )
   LET edges = (
     FOR edge IN djornl_edge
       FILTER edge._from IN node_ids AND edge._to IN node_ids
+        AND (length(@edge_types) == 0 || edge.edge_type IN @edge_types)
       RETURN edge
   )
   LET nodes = (

spec/stored_queries/djornl/djornl_fetch_phenotypes.yaml

@@ -14,17 +14,21 @@ params:
       examples: [["As2"],["As2", "Na23"]]
     distance:
       $ref: "../../datasets/distance.yaml"
+    edge_types:
+      $ref: "../../datasets/djornl/edge_types_filter.yaml"
 query: |
   LET node_ids = (
     FOR n IN djornl_node
       FILTER n._key IN @keys AND n.node_type == 'pheno'
-      FOR node IN 0..@distance ANY n djornl_edge
+      FOR v, e, p IN 0..@distance ANY n djornl_edge
         OPTIONS {bfs: true, uniqueVertices: "global"}
-        RETURN DISTINCT node._id
+        FILTER length(@edge_types) == 0 || p.edges[*].edge_type ALL IN @edge_types
+        RETURN DISTINCT v._id
   )
   LET edges = (
     FOR edge IN djornl_edge
       FILTER edge._from IN node_ids AND edge._to IN node_ids
+        AND (length(@edge_types) == 0 || edge.edge_type IN @edge_types)
       RETURN edge
   )
   LET nodes = (

spec/stored_queries/djornl/djornl_search_nodes.yaml

@@ -11,6 +11,8 @@ params:
       examples: ['GO:0005515', 'organelle machinery']
     distance:
       $ref: "../../datasets/distance.yaml"
+    edge_types:
+      $ref: "../../datasets/djornl/edge_types_filter.yaml"
 query: |
   LET node_ids = (
     FOR g IN djornl_node_view
@@ -29,13 +31,15 @@ query: |
         )
         OR PHRASE(g.go_terms, @search_text)
         OR PHRASE(g.transcript, @search_text)
-      FOR node IN 0..@distance ANY g djornl_edge
+      FOR v, e, p IN 0..@distance ANY g djornl_edge
         OPTIONS {bfs: true, uniqueVertices: "global"}
-        RETURN DISTINCT node._id
+        FILTER length(@edge_types) == 0 || p.edges[*].edge_type ALL IN @edge_types
+        RETURN DISTINCT v._id
   )
   LET edges = (
     FOR edge IN djornl_edge
       FILTER edge._from IN node_ids AND edge._to IN node_ids
+        AND (length(@edge_types) == 0 || edge.edge_type IN @edge_types)
       RETURN edge
   )
   LET nodes = (