From c0039d34b6991508961c82cdda2deb852d018f7c Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 1 Feb 2024 16:04:48 -0500
Subject: [PATCH 1/8] style: formatting

---
 src/transformers/jq_transformer.ts |  26 +++--
 src/transformers/transformer.ts    | 160 ++++++++++++++++++++---------
 2 files changed, 132 insertions(+), 54 deletions(-)

diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index 1da932d..f9c2865 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -11,21 +11,28 @@ import { toArray } from "../utils";
 const filterStringsWrap = Object.fromEntries(
   fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/wrap`)).map(file => {
     const filePath = Path.resolve(`${__dirname}/../../data/jq/wrap/${file}`);
-    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+    return [
+      Path.parse(filePath).name,
+      fs.readFileSync(filePath, { encoding: "utf8" }),
+    ];
   }),
 );
 
 const filterStringsPair = Object.fromEntries(
   fs.readdirSync(Path.resolve(`${__dirname}/../../data/jq/pair`)).map(file => {
     const filePath = Path.resolve(`${__dirname}/../../data/jq/pair/${file}`);
-    return [Path.parse(filePath).name, fs.readFileSync(filePath, { encoding: "utf8" })];
+    return [
+      Path.parse(filePath).name,
+      fs.readFileSync(filePath, { encoding: "utf8" }),
+    ];
   }),
 );
 
 export default class JQTransformer extends BaseTransformer {
   // TODO more specific typing?
   async wrap(res: JSONDoc | JSONDoc[]): Promise<JSONDoc> {
-    let filterString: string | undefined = this.config.wrap ?? filterStringsWrap[this.config.type];
+    let filterString: string | undefined =
+      this.config.wrap ?? filterStringsWrap[this.config.type];
     if (typeof filterString === "undefined") return super.wrap(res);
     filterString = generateFilterString(filterString);
     return JSON.parse(
@@ -36,8 +43,10 @@ export default class JQTransformer extends BaseTransformer {
   }
 
   async pairCurieWithAPIResponse(): Promise<PairedResponse> {
-    let filterString: string | undefined = this.config.pair ?? filterStringsPair[this.config.type];
-    if (typeof filterString === "undefined") return super.pairCurieWithAPIResponse();
+    let filterString: string | undefined =
+      this.config.pair ?? filterStringsPair[this.config.type];
+    if (typeof filterString === "undefined")
+      return super.pairCurieWithAPIResponse();
     const data = {
       response: this.data.response,
       edge: {
@@ -49,7 +58,8 @@ export default class JQTransformer extends BaseTransformer {
           type: this.edge.association.input_type,
           // input is array or is object with queryInputs
           curies:
-            Array.isArray(this.edge.input) || typeof this.edge.input === "string"
+            Array.isArray(this.edge.input) ||
+              typeof this.edge.input === "string"
               ? toArray(this.edge.input)
               : toArray(this.edge.input.queryInputs),
         },
@@ -61,6 +71,8 @@ export default class JQTransformer extends BaseTransformer {
       },
     };
     filterString = `.edge as $edge | ${generateFilterString(filterString)}`;
-    return JSON.parse((await jq.run(filterString, data, { input: "json" })) as string);
+    return JSON.parse(
+      (await jq.run(filterString, data, { input: "json" })) as string,
+    );
   }
 }
diff --git a/src/transformers/transformer.ts b/src/transformers/transformer.ts
index a07b4a4..02f1df3 100644
--- a/src/transformers/transformer.ts
+++ b/src/transformers/transformer.ts
@@ -24,9 +24,11 @@ export default class BaseTransformer {
    * Create an object with key representing input, and value representing the output of API
    */
   async pairCurieWithAPIResponse() {
-    let input = generateCurie(
+    const input = generateCurie(
       this.edge.association.input_id,
-      this.edge.input.hasOwnProperty("queryInputs") ? this.edge.input["queryInputs"] : (this.edge.input as string),
+      this.edge.input.hasOwnProperty("queryInputs")
+        ? this.edge.input["queryInputs"]
+        : (this.edge.input as string),
     );
     return {
       [input]: [this.data.response],
@@ -71,12 +73,18 @@ export default class BaseTransformer {
       {
         prop: "ref_pmcid",
         prefix: "PMCID:",
-        urls: ["http://www.ncbi.nlm.nih.gov/pmc/articles/", "http://europepmc.org/articles/"],
+        urls: [
+          "http://www.ncbi.nlm.nih.gov/pmc/articles/",
+          "http://europepmc.org/articles/",
+        ],
       },
       {
         prop: "ref_clinicaltrials",
         prefix: "clinicaltrials:",
-        urls: ["https://clinicaltrials.gov/ct2/show/", "https://www.clinicaltrials.gov/ct2/show/"],
+        urls: [
+          "https://clinicaltrials.gov/ct2/show/",
+          "https://www.clinicaltrials.gov/ct2/show/",
+        ],
       },
       {
         prop: "ref_doi",
@@ -88,29 +96,37 @@ export default class BaseTransformer {
           "http://onlinelibrary.wiley.com/doi/",
         ],
       },
-      { prop: "ref_isbn", prefix: "isbn:", urls: ["https://www.isbn-international.org/identifier/"] },
+      {
+        prop: "ref_isbn",
+        prefix: "isbn:",
+        urls: ["https://www.isbn-international.org/identifier/"],
+      },
     ];
 
     // handle URLs (which could be CURIEs)
     if ("ref_url" in mappedResponse) {
-      for (let publication of toArray(mappedResponse.ref_url)) {
+      for (const publication of toArray(mappedResponse.ref_url)) {
         if (typeof publication !== "string" || publication.length === 0) {
           continue;
         }
 
         let isCurie = false;
-        for (let publicationType of publicationTypes) {
-          for (let url of publicationType.urls) {
+        for (const publicationType of publicationTypes) {
+          for (const url of publicationType.urls) {
             if (publication.startsWith(url)) {
               isCurie = true;
 
               if (!mappedResponse[publicationType.prop]) {
                 mappedResponse[publicationType.prop] = [];
               } else if (!Array.isArray(mappedResponse[publicationType.prop])) {
-                mappedResponse[publicationType.prop] = toArray(mappedResponse[publicationType.prop]);
+                mappedResponse[publicationType.prop] = toArray(
+                  mappedResponse[publicationType.prop],
+                );
               }
 
-              mappedResponse[publicationType.prop].push(publication.slice(url.length));
+              mappedResponse[publicationType.prop].push(
+                publication.slice(url.length),
+              );
 
               break;
             }
@@ -128,7 +144,7 @@ export default class BaseTransformer {
     }
     delete mappedResponse.ref_url;
 
-    for (let publicationType of publicationTypes) {
+    for (const publicationType of publicationTypes) {
       if (publicationType.prop in mappedResponse) {
         for (let publication of toArray(mappedResponse[publicationType.prop])) {
           // handle numbers
@@ -140,10 +156,19 @@ export default class BaseTransformer {
             continue;
           }
 
-          if (publication.toUpperCase().startsWith(publicationType.prefix.toUpperCase())) {
-            mappedResponse.publications.push(publicationType.prefix + publication.slice(publicationType.prefix.length));
+          if (
+            publication
+              .toUpperCase()
+              .startsWith(publicationType.prefix.toUpperCase())
+          ) {
+            mappedResponse.publications.push(
+              publicationType.prefix +
+              publication.slice(publicationType.prefix.length),
+            );
           } else {
-            mappedResponse.publications.push(publicationType.prefix + publication);
+            mappedResponse.publications.push(
+              publicationType.prefix + publication,
+            );
           }
         }
 
@@ -170,16 +195,26 @@ export default class BaseTransformer {
   _getSubject(subjectCurie: any) {
     //debug(`input: ${input}`);
     let subject = {
-      original: typeof this.edge.original_input === "undefined" ? undefined : this.edge.original_input[subjectCurie],
+      original:
+        typeof this.edge.original_input === "undefined"
+          ? undefined
+          : this.edge.original_input[subjectCurie],
       // normalizedInfo:
       //     typeof this.edge.input_resolved_identifiers === "undefined" || typeof this.edge.original_input === "undefined"
       //     ? undefined
       //     : this.edge.input_resolved_identifiers[this.edge.original_input[subjectCurie]],
     };
-    if (this.edge.input_resolved_identifiers && subject.original === undefined) {
+    if (
+      this.edge.input_resolved_identifiers &&
+      subject.original === undefined
+    ) {
       //try to find an equivalent ids object if the original input doesn't match (for ICEES)
-      for (let curie of Object.keys(this.edge.input_resolved_identifiers)) {
-        if (this.edge.input_resolved_identifiers[curie].equivalentIDs.includes(subjectCurie)) {
+      for (const curie of Object.keys(this.edge.input_resolved_identifiers)) {
+        if (
+          this.edge.input_resolved_identifiers[curie].equivalentIDs.includes(
+            subjectCurie,
+          )
+        ) {
           subject = {
             original: curie,
             // normalizedInfo: this.edge.input_resolved_identifiers[curie],
@@ -204,7 +239,10 @@ export default class BaseTransformer {
    * @param {Object} mappedResponse - JSON response representing an output.
    */
   async formatRecords(subjectCurie: string, mappedResponse: any) {
-    if (mappedResponse === undefined || Object.keys(mappedResponse).length === 0) {
+    if (
+      mappedResponse === undefined ||
+      Object.keys(mappedResponse).length === 0
+    ) {
       return [];
     }
 
@@ -222,16 +260,24 @@ export default class BaseTransformer {
       mappedResponse: { ...mappedResponse },
     };
 
-    let transformedRecords = await async.mapSeries(objectIDs, async (curie: string) => {
-      let copyRecord = {
-        ...frozenRecord,
-        object: {
-          original: curie,
-          apiLabel: outputName,
-        },
-      };
-      return new Record(copyRecord, this.config, this.edge.association, this.edge.reasoner_edge);
-    });
+    const transformedRecords = await async.mapSeries(
+      objectIDs,
+      async (curie: string) => {
+        const copyRecord = {
+          ...frozenRecord,
+          object: {
+            original: curie,
+            apiLabel: outputName,
+          },
+        };
+        return new Record(
+          copyRecord,
+          this.config,
+          this.edge.association,
+          this.edge.reasoner_edge,
+        );
+      },
+    );
     return transformedRecords;
   }
 
@@ -239,25 +285,43 @@ export default class BaseTransformer {
    * Main function to transform API response
    */
   async transform() {
-    let transformedRecords = [];
-    let responses = await this.pairCurieWithAPIResponse();
+    const transformedRecords = [];
+    const responses = await this.pairCurieWithAPIResponse();
 
-    await async.eachSeries(Object.entries(responses), async ([curie, curieResponses]) => {
-      if (Array.isArray(curieResponses) && curieResponses.length > 0) {
-        await async.eachSeries(curieResponses, async response => {
-          const predicateResponse = this.jsonTransform(await this.wrap(response));
-          await async.eachSeries(Object.entries(predicateResponse), async ([predicate, mappedResponses]) => {
-            if (Array.isArray(mappedResponses) && mappedResponses.length > 0) {
-              await async.eachSeries(mappedResponses, async (mappedResponse: any[]) => {
-                transformedRecords.push(...(await this.formatRecords(curie, mappedResponse)));
-              });
-            } else {
-              transformedRecords.push(...(await this.formatRecords(curie, mappedResponses)));
-            }
+    await async.eachSeries(
+      Object.entries(responses),
+      async ([curie, curieResponses]) => {
+        if (Array.isArray(curieResponses) && curieResponses.length > 0) {
+          await async.eachSeries(curieResponses, async response => {
+            const predicateResponse = this.jsonTransform(
+              await this.wrap(response),
+            );
+            await async.eachSeries(
+              Object.entries(predicateResponse),
+              async ([predicate, mappedResponses]) => {
+                if (
+                  Array.isArray(mappedResponses) &&
+                  mappedResponses.length > 0
+                ) {
+                  await async.eachSeries(
+                    mappedResponses,
+                    async (mappedResponse: any[]) => {
+                      transformedRecords.push(
+                        ...(await this.formatRecords(curie, mappedResponse)),
+                      );
+                    },
+                  );
+                } else {
+                  transformedRecords.push(
+                    ...(await this.formatRecords(curie, mappedResponses)),
+                  );
+                }
+              },
+            );
           });
-        });
-      }
-    });
+        }
+      },
+    );
     return transformedRecords;
   }
 
@@ -271,6 +335,8 @@ export default class BaseTransformer {
       return [];
     }
     mappedResponse[output_id_type] = toArray(mappedResponse[output_id_type]);
-    return mappedResponse[output_id_type].map((id: string) => generateCurie(output_id_type, id));
+    return mappedResponse[output_id_type].map((id: string) =>
+      generateCurie(output_id_type, id),
+    );
   }
 }

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 2/8] 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" });

From 1cddaf64cd5e1aa4a650710431847d188f1e8811 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Tue, 6 Feb 2024 15:15:57 -0800
Subject: [PATCH 3/8] feat: add response mapping to edge data

---
 src/transformers/jq_transformer.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index f9c2865..199df15 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -68,6 +68,7 @@ export default class JQTransformer extends BaseTransformer {
           id: this.edge.association.output_id,
           type: this.edge.association.output_type,
         },
+        response_mapping: this.edge.response_mapping,
       },
     };
     filterString = `.edge as $edge | ${generateFilterString(filterString)}`;

From a9551e95fbd749b0916e43e285fa2eda563e6c29 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Tue, 6 Feb 2024 15:16:10 -0800
Subject: [PATCH 4/8] feat: update monarch jq

---
 data/jq/pair/monarch.jq | 27 ++++++++++-----------------
 1 file changed, 10 insertions(+), 17 deletions(-)

diff --git a/data/jq/pair/monarch.jq b/data/jq/pair/monarch.jq
index bf6d05a..a77ebf2 100644
--- a/data/jq/pair/monarch.jq
+++ b/data/jq/pair/monarch.jq
@@ -1,21 +1,15 @@
-generateCurie($edge.input.id; $edge.input.curies) as $input_curie 
-| .response.items = [
-  .response.items[]
+.response as $response
+| generateCurie($edge.input.id; $edge.input.curies) as $input_curie 
+| if $edge.response_mapping[$edge.predicate].output_name | contains("object")
+  then "object_namespace"
+  else "subject_namespace"
+  end 
+| . as $output_namespace
+| { $input_curie: [$response] } | .[$input_curie][0].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 == $edge.output.id
+    .[$output_namespace] == $edge.output.id
   ) 
   | .publications = [
     if .publications != null
@@ -26,4 +20,3 @@ generateCurie($edge.input.id; $edge.input.curies) as $input_curie
     | select(. | startswith("PMID:"))
   ]
 ]
-| { $input_curie: [.response] }

From 33b79c039c05821f33cb0d2eb351d21f5f956a2e Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 15 Feb 2024 12:48:04 -0500
Subject: [PATCH 5/8] feat: provide $response variable to jq strings

---
 src/transformers/jq_transformer.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/transformers/jq_transformer.ts b/src/transformers/jq_transformer.ts
index 199df15..444429a 100644
--- a/src/transformers/jq_transformer.ts
+++ b/src/transformers/jq_transformer.ts
@@ -71,7 +71,7 @@ export default class JQTransformer extends BaseTransformer {
         response_mapping: this.edge.response_mapping,
       },
     };
-    filterString = `.edge as $edge | ${generateFilterString(filterString)}`;
+    filterString = `.edge as $edge | .response as $response | ${generateFilterString(filterString)}`;
     return JSON.parse(
       (await jq.run(filterString, data, { input: "json" })) as string,
     );

From cc21854e71e1e85db167c861a3431e7ab87ae229 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Thu, 15 Feb 2024 12:48:30 -0500
Subject: [PATCH 6/8] feat: transform sources for BTE ingestion

---
 data/jq/pair/monarch.jq | 31 +++++++++++++++++++++++++++++--
 1 file changed, 29 insertions(+), 2 deletions(-)

diff --git a/data/jq/pair/monarch.jq b/data/jq/pair/monarch.jq
index a77ebf2..d9bac72 100644
--- a/data/jq/pair/monarch.jq
+++ b/data/jq/pair/monarch.jq
@@ -1,5 +1,4 @@
-.response as $response
-| generateCurie($edge.input.id; $edge.input.curies) as $input_curie 
+generateCurie($edge.input.id; $edge.input.curies) as $input_curie 
 | if $edge.response_mapping[$edge.predicate].output_name | contains("object")
   then "object_namespace"
   else "subject_namespace"
@@ -19,4 +18,32 @@
     | .[]
     | select(. | startswith("PMID:"))
   ]
+  | .primary_knowledge_source as $primary_knowledge_source
+  | .sources = (
+    if .primary_knowledge_source != null and .aggregator_knowledge_source != null
+    then
+      [
+        {
+          resource_role: "primary_knowledge_source",
+          resource_id: $primary_knowledge_source
+        }
+      ] 
+      + (.aggregator_knowledge_source | reverse | reduce .[] as $source (
+        null; 
+        if . == null
+        then [{
+          resource_role: "aggregator_knowledge_source", 
+          resource_id: $source,
+          upstream_resource_ids: [$primary_knowledge_source]
+        }]
+        else . + [{
+          resource_role: "aggregator_knowledge_source",
+          resource_id: $source,
+          upstream_resource_ids: [.[-1].resource_id]
+        }]
+        end
+      ))
+    else [{ resource_role: "primary_knowledge_source", resource_id:"infores:monarchinitiative" }]
+    end
+  )
 ]

From 3534b23f1b6467eb464757e366414fe84a692233 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Tue, 20 Feb 2024 16:05:59 -0500
Subject: [PATCH 7/8] fix: record uses source in hash

---
 src/record.ts | 165 ++++++++++++++++++++++++++++++++++++--------------
 1 file changed, 119 insertions(+), 46 deletions(-)

diff --git a/src/record.ts b/src/record.ts
index 7602d83..e1a7b2f 100644
--- a/src/record.ts
+++ b/src/record.ts
@@ -11,14 +11,21 @@ export class RecordNode {
   _qNode: QNode;
   _apiLabel: string;
 
-  constructor(node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode, qNode: QNode) {
+  constructor(
+    node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode,
+    qNode: QNode,
+  ) {
     this.original = node.original;
-    this.normalizedInfo = node.normalizedInfo ? node.normalizedInfo : this.makeFakeInfo(node);
+    this.normalizedInfo = node.normalizedInfo
+      ? node.normalizedInfo
+      : this.makeFakeInfo(node);
     this._qNode = qNode;
     this._apiLabel = node.apiLabel;
   }
 
-  makeFakeInfo(node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode): NodeNormalizerResultObj {
+  makeFakeInfo(
+    node: FrozenNode | VerboseFrozenNode | MinimalFrozenNode,
+  ): NodeNormalizerResultObj {
     return {
       primaryID: node.curie,
       equivalentIDs: node.equivalentCuries ?? [],
@@ -82,19 +89,30 @@ export class RecordNode {
 
   get UMLS(): string[] {
     return (
-      this.normalizedInfo?.equivalentIDs.reduce((arr: string[], curie: string) => {
-        if (curie.includes("UMLS")) arr.push(curie.replace("UMLS:", ""));
-        return arr;
-      }, []) ?? []
+      this.normalizedInfo?.equivalentIDs.reduce(
+        (arr: string[], curie: string) => {
+          if (curie.includes("UMLS")) arr.push(curie.replace("UMLS:", ""));
+          return arr;
+        },
+        [],
+      ) ?? []
     );
   }
 
   get semanticType(): string[] {
-    return this.normalizedInfo?.primaryTypes.map(semanticType => `biolink:${semanticType}`) ?? [];
+    return (
+      this.normalizedInfo?.primaryTypes.map(
+        semanticType => `biolink:${semanticType}`,
+      ) ?? []
+    );
   }
 
   get semanticTypes(): string[] {
-    return this.normalizedInfo?.semanticTypes.map(semanticType => `biolink:${semanticType}`) ?? [];
+    return (
+      this.normalizedInfo?.semanticTypes.map(
+        semanticType => `biolink:${semanticType}`,
+      ) ?? []
+    );
   }
 
   get label(): string {
@@ -157,30 +175,39 @@ export class Record {
     reversedAPIEdge.input_type = frozen.association.output_type;
     reversedAPIEdge.output_id = frozen.association.input_id;
     reversedAPIEdge.output_type = frozen.association.input_type;
-    const predicate = this.qEdge.getReversedPredicate(frozen.association.predicate);
+    const predicate = this.qEdge.getReversedPredicate(
+      frozen.association.predicate,
+    );
     reversedAPIEdge.predicate = predicate;
     if (reversedAPIEdge.qualifiers) {
       const reversedQualifiers = Object.fromEntries(
-        Object.entries(reversedAPIEdge.qualifiers).map(([qualifierType, qualifier]) => {
-          let newQualifierType: string = qualifierType;
-          let newQualifier: string | string[] = qualifier;
-          if (qualifierType.includes("predicate")) {
-            if (Array.isArray(qualifier)) {
-              newQualifier = qualifier.map(
-                (str: string) => `biolink:${this.qEdge.getReversedPredicate(str.replace("biolink:", ""))}`,
-              );
-            } else {
-              newQualifier = `biolink:${this.qEdge.getReversedPredicate(qualifier.replace("biolink:", ""))}`;
+        Object.entries(reversedAPIEdge.qualifiers).map(
+          ([qualifierType, qualifier]) => {
+            let newQualifierType: string = qualifierType;
+            let newQualifier: string | string[] = qualifier;
+            if (qualifierType.includes("predicate")) {
+              if (Array.isArray(qualifier)) {
+                newQualifier = qualifier.map(
+                  (str: string) =>
+                    `biolink:${this.qEdge.getReversedPredicate(
+                      str.replace("biolink:", ""),
+                    )}`,
+                );
+              } else {
+                newQualifier = `biolink:${this.qEdge.getReversedPredicate(
+                  qualifier.replace("biolink:", ""),
+                )}`;
+              }
             }
-          }
-          if (qualifierType.includes("subject")) {
-            newQualifierType = qualifierType.replace("subject", "object");
-          }
-          if (qualifierType.includes("object")) {
-            newQualifierType = qualifierType.replace("object", "subject");
-          }
-          return [newQualifierType, newQualifier];
-        }),
+            if (qualifierType.includes("subject")) {
+              newQualifierType = qualifierType.replace("subject", "object");
+            }
+            if (qualifierType.includes("object")) {
+              newQualifierType = qualifierType.replace("object", "subject");
+            }
+            return [newQualifierType, newQualifier];
+          },
+        ),
       );
 
       reversedAPIEdge.qualifiers = reversedQualifiers;
@@ -191,7 +218,13 @@ export class Record {
     const temp = frozen.subject;
     frozen.subject = frozen.object;
     frozen.object = temp;
-    return new Record(frozen, this.config, frozen.association, this.qEdge, !this.reverseToExecution);
+    return new Record(
+      frozen,
+      this.config,
+      frozen.association,
+      this.qEdge,
+      !this.reverseToExecution,
+    );
   }
 
   queryDirection() {
@@ -203,7 +236,9 @@ export class Record {
   }
 
   // for user-made records lacking qEdge
-  makeFakeQEdge(record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord): QEdge {
+  makeFakeQEdge(
+    record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord,
+  ): QEdge {
     return {
       getID(): string {
         return "fakeEdge";
@@ -244,14 +279,18 @@ export class Record {
     };
   }
 
-  makeAPIEdge(record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord): Association {
+  makeAPIEdge(
+    record: FrozenRecord | VerboseFrozenRecord | MinimalFrozenRecord,
+  ): Association {
     return {
       predicate: record.predicate?.replace("biolink:", ""),
       qualifiers: record.qualifiers
         ? Object.fromEntries(
-          Object.entries(record.qualifiers).map(([qualifierType, qualifier]: [string, string]) => {
-            return [qualifierType.replace("biolink:", ""), qualifier];
-          }),
+          Object.entries(record.qualifiers).map(
+            ([qualifierType, qualifier]: [string, string]) => {
+              return [qualifierType.replace("biolink:", ""), qualifier];
+            },
+          ),
         )
         : undefined,
       api_name: record.api,
@@ -267,8 +306,13 @@ export class Record {
     return records.map((record: Record): FrozenRecord => record.freeze());
   }
 
-  public static unfreezeRecords(records: FrozenRecord[], config?: any): Record[] {
-    return records.map((record: FrozenRecord): Record => new Record(record, config));
+  public static unfreezeRecords(
+    records: FrozenRecord[],
+    config?: any,
+  ): Record[] {
+    return records.map(
+      (record: FrozenRecord): Record => new Record(record, config),
+    );
   }
 
   public static packRecords(records: Record[]): RecordPackage {
@@ -281,7 +325,9 @@ export class Record {
 
       const apiEdgeHash = hash(JSON.stringify(record.association));
 
-      let apiEdgeHashIndex = apiEdgeHashes.findIndex(hash => hash === apiEdgeHash);
+      let apiEdgeHashIndex = apiEdgeHashes.findIndex(
+        hash => hash === apiEdgeHash,
+      );
 
       if (apiEdgeHashIndex === -1) {
         apiEdgeHashes.push(apiEdgeHash);
@@ -298,7 +344,11 @@ export class Record {
     return [apiEdges, ...frozenRecords];
   }
 
-  public static unpackRecords(recordPack: RecordPackage, qEdge: QEdge, config?: any): Record[] {
+  public static unpackRecords(
+    recordPack: RecordPackage,
+    qEdge: QEdge,
+    config?: any,
+  ): Record[] {
     const [apiEdges, ...frozenRecords] = recordPack;
     return frozenRecords.map((record: any): Record => {
       const apiEdge = apiEdges[record.apiEdge];
@@ -353,7 +403,10 @@ export class Record {
     return attributes
       ? attributes.reduce((arr: EdgeAttribute[], attribute: EdgeAttribute) => {
         attribute.attributes
-          ? arr.push(attribute, ...this._getFlattenedEdgeAttributes(attribute.attributes))
+          ? arr.push(
+            attribute,
+            ...this._getFlattenedEdgeAttributes(attribute.attributes),
+          )
           : arr.push(attribute);
         return arr;
       }, [])
@@ -361,9 +414,13 @@ export class Record {
   }
 
   get _configuredEdgeAttributesForHash(): string {
-    return this._getFlattenedEdgeAttributes(this.mappedResponse["edge-attributes"])
+    return this._getFlattenedEdgeAttributes(
+      this.mappedResponse["edge-attributes"],
+    )
       .filter(attribute => {
-        return this.config?.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?.includes(attribute.attribute_type_id);
+        return this.config?.EDGE_ATTRIBUTES_USED_IN_RECORD_HASH?.includes(
+          attribute.attribute_type_id,
+        );
       })
       .reduce((acc, attribute) => {
         return [...acc, `${attribute.attribute_type_id}:${attribute.value}`];
@@ -378,10 +435,19 @@ export class Record {
       this.object.curie,
       Object.entries(this.qualifiers)
         .sort(([qTa, qVa], [qTb, qVb]) => qTa.localeCompare(qTb))
-        .reduce((str, [qualifierType, qualifierValue]) => `${str};${qualifierType}:${qualifierValue}`, ""),
+        .reduce(
+          (str, [qualifierType, qualifierValue]) =>
+            `${str};${qualifierType}:${JSON.stringify(qualifierValue)}`,
+          "",
+        ),
       this.api,
       this.metaEdgeSource,
       this._configuredEdgeAttributesForHash,
+      JSON.stringify(
+        this.provenanceChain.sort((sourceA, sourceB) =>
+          sourceA.resource_id.localeCompare(sourceB.resource_id),
+        ),
+      ),
     ].join("-");
   }
 
@@ -399,11 +465,16 @@ export class Record {
     }
     return Object.fromEntries(
       Object.entries(this._qualifiers).map(([qualifierType, qualifier]) => {
-        const newQualifierType = `biolink:${qualifierType.replace("biolink:", "")}`;
+        const newQualifierType = `biolink:${qualifierType.replace(
+          "biolink:",
+          "",
+        )}`;
         let newQualifier = qualifier;
         if (qualifierType.includes("predicate")) {
           if (Array.isArray(qualifier)) {
-            newQualifier = qualifier.map(str => `biolink:${str.replace("biolink", "")}`);
+            newQualifier = qualifier.map(
+              str => `biolink:${str.replace("biolink", "")}`,
+            );
           } else {
             newQualifier = `biolink:${qualifier.replace("biolink:", "")}`;
           }
@@ -434,7 +505,9 @@ export class Record {
       returnValue = _.cloneDeep(this.mappedResponse.trapi_sources);
     } else {
       returnValue.push({
-        resource_id: this.association.apiIsPrimaryKnowledgeSource ? this.apiInforesCurie : this.metaEdgeSource,
+        resource_id: this.association.apiIsPrimaryKnowledgeSource
+          ? this.apiInforesCurie
+          : this.metaEdgeSource,
         resource_role: "primary_knowledge_source",
       });
       if (!this.association.apiIsPrimaryKnowledgeSource) {

From e117b3710831be3cd05e49ccd15f56a0fbbb0314 Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Wed, 21 Feb 2024 14:39:22 -0500
Subject: [PATCH 8/8] chore: rm check matching namespace (query handled)

---
 data/jq/pair/monarch.jq | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/data/jq/pair/monarch.jq b/data/jq/pair/monarch.jq
index d9bac72..dc5e0ff 100644
--- a/data/jq/pair/monarch.jq
+++ b/data/jq/pair/monarch.jq
@@ -7,9 +7,9 @@ generateCurie($edge.input.id; $edge.input.curies) as $input_curie
 | { $input_curie: [$response] } | .[$input_curie][0].items = [
   $response.items[]
   | select(. != null)
-  | select(
-    .[$output_namespace] == $edge.output.id
-  ) 
+  # | select(
+  #   .[$output_namespace] == $edge.output.id
+  # ) 
   | .publications = [
     if .publications != null
     then .publications