From d6014a65752afca8f4bec63273173103623b769e Mon Sep 17 00:00:00 2001
From: Jackson Callaghan <43009413+tokebe@users.noreply.github.com>
Date: Tue, 22 Oct 2024 15:21:55 -0400
Subject: [PATCH] Revert "semmed sentence edge attributes"

---
 data/jq/pair/semmed.jq | 23 -----------------------
 data/jq/wrap/semmed.jq | 29 -----------------------------
 src/index.ts           |  2 --
 3 files changed, 54 deletions(-)
 delete mode 100644 data/jq/pair/semmed.jq
 delete mode 100644 data/jq/wrap/semmed.jq

diff --git a/data/jq/pair/semmed.jq b/data/jq/pair/semmed.jq
deleted file mode 100644
index 1b61745..0000000
--- a/data/jq/pair/semmed.jq
+++ /dev/null
@@ -1,23 +0,0 @@
-if $edge.query.method == "post" then
-  # if response is not an array, then use response.hits
-  if (.response | type) == "array" then .response else .response.hits end |
-  reduce .[] as $item ({};
-    # if the item is notfound, then proceed to next item & keep current object
-    if ($item | keys | contains(["notfound"])) then
-      .
-    else
-      generateCurieWithInputs(
-        $edge.input.id;
-        $item.query; 
-        $edge.input.curies
-        | toArray
-        | map(. | split(":") | last)
-      ) as $curie | .[$curie] += [$item]
-    end
-  )
-else
-  .response as $res | generateCurie(
-    $edge.input.id;
-    ($edge.input.curies | toArray | map(. | split(":") | last) | first)
-  ) as $curie | {} | .[$curie] = [$res]
-end
diff --git a/data/jq/wrap/semmed.jq b/data/jq/wrap/semmed.jq
deleted file mode 100644
index 8ee6b68..0000000
--- a/data/jq/wrap/semmed.jq
+++ /dev/null
@@ -1,29 +0,0 @@
-# finds start/end index of sub in main string
-# ie. "ab" in "12abcd" will return "2|3"
-def index_text(main; sub): (main|index(sub)|tostring)+"|"+((main|index(sub)) + (sub|length) | tostring);
-
-
-.["edge-attributes"] = ([.predication | group_by(.pmid) | .[] | .[0] |
-# create edge attributes for each publication
-{
-  "attribute_type_id": "biolink:has_supporting_study_result",
-  "attributes": [
-    {
-      "attribute_type_id": "biolink:supporting_text",
-      "value": .sentence,
-    },
-    {
-      "attribute_type_id": "biolink:publications",
-      "value": ( "PMID:"+(.pmid|tostring) ),
-    },
-    {
-      "attribute_type_id": "biolink:subject_location_in_text",
-      "value": ( .subject_text as $text | index_text(.sentence; $text) ),
-    },
-    {
-      "attribute_type_id": "biolink:object_location_in_text",
-      "value": ( .object_text as $text | index_text(.sentence; $text) ),
-    }
-  ],
-  "value": ( .predication_id | tostring ),
-}] | .[:50])
diff --git a/src/index.ts b/src/index.ts
index cde90e7..68b99fd 100644
--- a/src/index.ts
+++ b/src/index.ts
@@ -50,8 +50,6 @@ export default class Transformer {
     } else if (api === "EBI Proteins API") {
       // this.tf = new EBIProteinTransformer(this.data, this.config)
       this.tf = new JQTransformer(this.data, { ...this.config, type: "ebi" });
-    } else if (api === "BioThings SEMMEDDB API") {
-      this.tf = new JQTransformer(this.data, { ...this.config, type: "semmed" });
     } else if (tags.includes("biothings")) {
       this.tf = new JQTransformer(this.data, { ...this.config, type: "biothings" });
     } else if (tags.includes("ctd")) {