From 80bdeb42193620aec1724150b09eece2d5a1d29a Mon Sep 17 00:00:00 2001
From: Rohan Juneja <rohanj2006@gmail.com>
Date: Mon, 4 Dec 2023 17:13:49 -0800
Subject: [PATCH] allow multiple input/output prefixes

---
 data/jq/utils.jq                | 5 ++++-
 src/transformers/transformer.ts | 9 +++++----
 src/types.ts                    | 3 +++
 src/utils.ts                    | 2 +-
 4 files changed, 13 insertions(+), 6 deletions(-)

diff --git a/data/jq/utils.jq b/data/jq/utils.jq
index 220755c..3f4abdd 100644
--- a/data/jq/utils.jq
+++ b/data/jq/utils.jq
@@ -16,8 +16,11 @@ def getfirst: if (. | type) == "array" then .[0] else . end;
 # generates a curie from a type and id
 def generateCurie(idType; id): id | getfirst | split(":") | last | idType + ":" + .;
 
+# removes prefix if there
+def rmPrefix: . | split(":") | last;
+
 # generates a curie from a type and id [string] (by checking queryInputs)
-def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[]) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
+def generateCurieWithInputs(idType; id; queryInputs): (id | getfirst) as $id | reduce (queryInputs | toArray | .[] | rmPrefix) as $input (""; if ($id | ascii_upcase | contains($input | ascii_upcase)) then $input else . end) | idType + ":" + .;
 
 # getting a nested field from inputted object (seperated by ., ie. drugcentral.bioactivity)
 def get_nested_field(field):
diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index a07b4a4..7d8f438 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -193,7 +193,7 @@ export default class BaseTransformer {
 
   _removeNonEdgeData(mappedResponse: any) {
     delete mappedResponse["@type"];
-    delete mappedResponse[this.edge.association.output_id];
+    delete mappedResponse["output"];
     delete mappedResponse["input_name"];
     delete mappedResponse["output_name"];
     return mappedResponse;
@@ -241,6 +241,7 @@ export default class BaseTransformer {
   async transform() {
     let transformedRecords = [];
     let responses = await this.pairCurieWithAPIResponse();
+    console.log((this.edge.input as any).queryInputs)
 
     await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
       if (Array.isArray(curieResponses) && curieResponses.length > 0) {
@@ -267,10 +268,10 @@ export default class BaseTransformer {
    */
   extractObjectIDs(mappedResponse: object) {
     const output_id_type = this.edge.association.output_id;
-    if (!(output_id_type in mappedResponse)) {
+    if (!('output' in mappedResponse)) {
       return [];
     }
-    mappedResponse[output_id_type] = toArray(mappedResponse[output_id_type]);
-    return mappedResponse[output_id_type].map((id: string) => generateCurie(output_id_type, id));
+    mappedResponse.output = toArray(mappedResponse['output']);
+    return (mappedResponse['output'] as any[]).map((id: string) => generateCurie(output_id_type, id));
   }
 }
diff --git a/src/types.ts b/src/types.ts
index 6c24101..74b5e89 100644
--- a/src/types.ts
+++ b/src/types.ts
@@ -3,7 +3,10 @@ import { JSONDoc } from "./json_transform/types";
 interface KGAssociationObject {
   input_id?: string;
   input_type: string;
+  input_name_field?: string;
   output_id?: string;
+  output_id_field: string;
+  output_name_field?: string;
   output_type: string;
   predicate: string;
   source?: string;
diff --git a/src/utils.ts b/src/utils.ts
index ffa9b24..67f66c5 100644
--- a/src/utils.ts
+++ b/src/utils.ts
@@ -8,7 +8,7 @@ export function generateCurie(idType: string, id: string | string[]) {
   return idType + ":" + id;
 }
 
-export function toArray(item) {
+export function toArray(item): any[] {
   if (!Array.isArray(item)) {
     return [item];
   }