old biolink -> new monarch

data/jq/pair/monarch.jq

@@ -0,0 +1,29 @@
+generateCurie($edge.input.id; $edge.input.curies) as $input_curie 
+| .response.items = [
+  .response.items[]
+  | select(. != null)
+  | select(
+    . as $item
+    | if $item.direction == "outgoing"
+      then $item.subject
+      else $item.object
+      end
+    | . as $input_curie
+    | if $item.direction == "outgoing"
+      then $item.object_namespace
+      else $item.subject_namespace
+      end
+    | . as $output_namespace
+    | $input_curie == $input_curie
+      and $output_namespace == $edge.output.id
+  ) 
+  | .publications = [
+    if .publications != null
+    then .publications
+    else []
+    end
+    | .[]
+    | select(. | startswith("PMID:"))
+  ]
+]
+| { $input_curie: [.response] }

src/index.ts

@@ -1,4 +1,3 @@
-import BiolinkTransformer from "./transformers/biolink_transformer";
 import BioThingsTransformer from "./transformers/biothings_transformer";
 // import CordTransformer from "./transformers/cord_transformer";
 import CTDTransformer from "./transformers/ctd_transformer";
@@ -46,9 +45,8 @@ export default class Transformer {
       this.tf = new TRAPITransformer(this.data, this.config);
     } else if (api.startsWith("SEMMED")) {
       this.tf = new SemmedTransformer(this.data, this.config);
-    } else if (api === "BioLink API") {
-      // this.tf = new BiolinkTransformer(this.data, this.config);
-      this.tf = new JQTransformer(this.data, { ...this.config, type: "biolink" });
+    } else if (api === "Monarch API") {
+      this.tf = new JQTransformer(this.data, { ...this.config, type: "monarch" });
     } else if (api === "EBI Proteins API") {
       // this.tf = new EBIProteinTransformer(this.data, this.config)
       this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" });