From a2dea9f2701b9cee62809b4cc4af3e73f1ede8c5 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 1 Feb 2024 16:05:07 -0500
Subject: [PATCH] old biolink -> new monarch

---
 data/jq/pair/monarch.jq | 29 +++++++++++++++++++++++++++++
 data/jq/wrap/biolink.jq | 18 ------------------
 src/index.ts            |  6 ++----
 3 files changed, 31 insertions(+), 22 deletions(-)
 create mode 100644 data/jq/pair/monarch.jq
 delete mode 100644 data/jq/wrap/biolink.jq

diff --git a/data/jq/pair/monarch.jq b/data/jq/pair/monarch.jq
new file mode 100644
index 0000000..bf6d05a
--- /dev/null
+++ b/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] }
diff --git a/data/jq/wrap/biolink.jq b/data/jq/wrap/biolink.jq
deleted file mode 100644
index 696d9d1..0000000
--- a/data/jq/wrap/biolink.jq
+++ /dev/null
@@ -1,18 +0,0 @@
-.associations = (
-  [
-    (
-      # take associations that aren't null
-      select(.associations != null) | .associations | .[] | 
-      # split association object ids & take last (only for CHEMBL, REACT, HGNC)
-      select(.object.id != null) | (.object.id | split(":") | first) as $pref | .object[$pref] = (if $pref == "HGNC" or $pref == "NCBIGene" or $pref == "REACT" then (.object.id | split(":") | last) else .object.id end) |
-      # take publications with PMID & for IDs take last element after splitting by :
-      .publications = [foreach (.publications | .[]? | .id) as $pub ([]; []; if ($pub == null or ($pub | startswith("PMID") | not)) then empty else {id: ($pub | split(":") | last)} end)]
-    )
-    # delete publications if empty array
-    | delifempty(.publications)
-  ] +
-  # include associations with null object ids
-  [select(.associations != null) | .associations | .[] | select(.object.id == null)]
-)
-# delete association if empty array
-| delifempty(.associations)
diff --git a/src/index.ts b/src/index.ts
index 1337221..68b99fd 100644
--- a/src/index.ts
+++ b/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" });