From e9e485afba48e1bf219ec7931b54deb3c52517a1 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 4 Nov 2024 10:47:08 -0800
Subject: [PATCH 01/29] Fix error catch/throw in uploadNormalizedVariant()

---
 src/civic/evidenceItem.js | 5 ++---
 src/civic/variant.js      | 7 ++++++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/src/civic/evidenceItem.js b/src/civic/evidenceItem.js
index f999f8db..0f49505a 100644
--- a/src/civic/evidenceItem.js
+++ b/src/civic/evidenceItem.js
@@ -180,9 +180,8 @@ const processCombination = async (conn, {
             const processedVariants = await processVariantRecord(conn, variant, feature);
             logger.verbose(`converted variant name (${variant.name}) to variants (${processedVariants.map(v => v.displayName).join(', and ')})`);
             variants.push(...processedVariants);
-        } catch (err) {
-            logger.error(`unable to process the variant (id=${rawRecord.variant.id}, name=${rawRecord.variant.name})`);
-            throw err;
+        } catch {
+            throw new Error(`unable to process the variant (id=${variant.id}, name=${variant.name})`);
         }
     }
 
diff --git a/src/civic/variant.js b/src/civic/variant.js
index 98ebee67..f66c011b 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -273,7 +273,11 @@ const uploadNormalizedVariant = async (conn, normalizedVariant, feature) => {
                 SOURCE_DEFN.name,
             );
         } catch (err) {
-            variantType = await conn.getVocabularyTerm(normalizedVariant.type || content.type);
+            try {
+                variantType = await conn.getVocabularyTerm(normalizedVariant.type || content.type);
+            } catch {
+                throw new Error(`Unable to upload CIVIC variant (${normalizedVariant}})`);
+            }
         }
         content.type = rid(variantType);
 
@@ -392,6 +396,7 @@ const processVariantRecord = async (conn, civicVariantRecord, feature) => {
         }
     } catch (err) {
         VARIANT_CACHE.set(JSON.stringify(rawVariant), { err });
+        throw err
     }
 
     VARIANT_CACHE.set(JSON.stringify(rawVariant), { result });

From fadc6e5898c12d506e26ff16d203c77e55ad227c Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 4 Nov 2024 10:50:15 -0800
Subject: [PATCH 02/29] Add getStatements() to civic/statements.js

---
 src/civic/statement.js | 39 +++++++++++++++++++++++++++------------
 1 file changed, 27 insertions(+), 12 deletions(-)

diff --git a/src/civic/statement.js b/src/civic/statement.js
index e4049bcf..cd83512d 100644
--- a/src/civic/statement.js
+++ b/src/civic/statement.js
@@ -177,6 +177,31 @@ const contentMatching = ({
     return records;
 };
 
+/**
+ * Given source & list of sourceIds, returns corresponding statements
+ *
+ * @param {ApiConnection} conn the api connection object for GraphKB
+ * @param {object} param1
+ * @param {string} param1.source the source RID
+ * @param {string[]} param1.sourceIds an array of sourceIds
+ * @returns {string[]} a list of statement RIDs
+ */
+const getStatements = async (conn, { source, sourceIds }) => {
+    const records = await conn.getRecords({
+        filters: {
+            AND: [
+                { sourceId: sourceIds },
+                { source },
+            ],
+        },
+        target: 'Statement',
+    });
+    const rids = records.map(
+        (el) => el['@rid'],
+    );
+    return rids;
+};
+
 /**
  * Given content from CIViC, try to create the GraphKB record
  *
@@ -250,18 +275,7 @@ const deleteStatements = async (conn, { rids = [], source, sourceIds }) => {
     // Get rids to delete if none provided
     if (rids.length === 0) {
         logger.info('Loading corresponding GraphKB statement RIDs to delete');
-        const records = await conn.getRecords({
-            filters: {
-                AND: [
-                    { sourceId: sourceIds },
-                    { source },
-                ],
-            },
-            target: 'Statement',
-        });
-        rids.push(...records.map(
-            (el) => el['@rid'],
-        ));
+        rids.push(...await getStatements(conn, { source, sourceIds }));
         logger.info(`${rids.length} RIDs found`);
     }
 
@@ -286,6 +300,7 @@ module.exports = {
     contentMatching,
     createStatement,
     deleteStatements,
+    getStatements,
     isMatching,
     needsUpdate,
     updateStatement,

From 626b50bdb1219e29865c2aa4733db6acc2d0d957 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 22 Nov 2024 10:00:47 -0800
Subject: [PATCH 03/29] Add --deleteDeprecated & --noDeleteOnUnmatched options
 to civic arg parser

---
 bin/load.js | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/bin/load.js b/bin/load.js
index 166ef615..ba3903d3 100644
--- a/bin/load.js
+++ b/bin/load.js
@@ -109,6 +109,16 @@ civicParser.add_argument('--noUpdate', {
     default: false,
     help: 'Will not check for updating content of existing GraphKB Statements',
 });
+civicParser.add_argument('--noDeleteOnUnmatched', {
+    action: 'store_true',
+    default: false,
+    help: 'Will not delete GraphKB Statements from valid sourceID but not matching a combination',
+});
+civicParser.add_argument('--deleteDeprecated', {
+    action: 'store_true',
+    default: false,
+    help: 'Will delete GraphKB Statements from deprecated sourceID',
+});
 
 const clinicaltrialsgovParser = subparsers.add_parser('clinicaltrialsgov');
 clinicaltrialsgovParser.add_argument('--days', {

From 214ebfc8976b22bf139ffdd30525536b07230f22 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 22 Nov 2024 10:07:35 -0800
Subject: [PATCH 04/29] Add support for noDeleteOnUnmatched option in civic

---
 src/civic/index.js | 25 +++++++++++++++++--------
 1 file changed, 17 insertions(+), 8 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 2f0aee38..f5611ec6 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -57,7 +57,8 @@ const incrementCounts = (initial, updates) => {
  * @param {ApiConnection} param0.conn the api connection object for GraphKB
  * @param {string} param0.errorLogPrefix prefix to the generated error json file
  * @param {number} param0.maxRecords limit of EvidenceItem records to be processed and upload
- * @param {?boolean} param0.noUpdate for avoiding deletion/update of existing GraphKB Statements
+ * @param {?boolean} param0.noDeleteOnUnmatched no deletion of existing GraphKB Statements related to unmatched combination(s)
+ * @param {?boolean} param0.noUpdate no update of existing GraphKB Statements
  * @param {string[]} param0.trustedCurators a list of curator IDs for submitted-only EvidenceItems
  * @param {?string} param0.url url to use as the base for accessing the civic ApiConnection
  */
@@ -65,6 +66,7 @@ const upload = async ({
     conn,
     errorLogPrefix,
     maxRecords,
+    noDeleteOnUnmatched = false,
     noUpdate = false,
     trustedCurators,
     url = BASE_URL,
@@ -181,7 +183,8 @@ const upload = async ({
         processingIntoCombinations: new Map(),
         relevance: new Map(),
     };
-    const casesToReview = new Map();
+    const statementsToReview_unmatched_processingError = new Map();
+    const statementsToReview_unmatched = new Map();
 
     logger.info(`\n\n${'#'.repeat(80)}\n## PROCESSING RECORDS\n${'#'.repeat(80)}\n`);
     let recordNumber = 0;
@@ -366,13 +369,17 @@ const upload = async ({
         }
 
         // DELETE
-        if (!noUpdate && toDelete.length > 0) {
+        if (toDelete.length > 0) {
             const rids = toDelete.map(el => el['@rid']);
 
             if (processCombinationErrors > 0) {
                 // Do not delete any statements if some combinations have processing errors
-                logger.info(`${toDelete.length} unmatched statement(s) to be reviewed for deletion`);
-                casesToReview.set(id, rids);
+                logger.warn(`${toDelete.length} unmatched statement(s). To be reviewed since some processing errors occured`);
+                statementsToReview_unmatched_processingError.set(id, rids);
+            } else if (noDeleteOnUnmatched) {
+                // Do not delete any statements if noDeleteOnUnmatched flag
+                logger.warn(`${toDelete.length} unmatched statement(s). To be reviewed since the noDeleteOnUnmatched flag is being used`);
+                statementsToReview_unmatched.set(id, rids);
             } else {
                 loaclCountsST.delete = await deleteStatements(conn, { rids });
             }
@@ -445,9 +452,11 @@ const upload = async ({
     // Logging processing error cases to be reviewed,
     // so a reviewer can decide if corresponding statements need to be deleted or not
     logger.info();
-    logger.info('***** Cases to be reviewed for deletion *****');
-    logger.warn(`${casesToReview.size} Evidence Item(s) with processing errors leading to unmatched Statement(s)`);
-    casesToReview.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
+    logger.info('***** Unmatched cases to be reviewed for deletion *****');
+    logger.warn(`${statementsToReview_unmatched_processingError.size} Evidence Item(s) with processing errors leading to unmatched Statement(s)`);
+    statementsToReview_unmatched_processingError.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
+    logger.warn(`${statementsToReview_unmatched.size} Evidence Item(s) with unmatched Statement(s) with no processing error involved`);
+    statementsToReview_unmatched.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
 
     // Logging Statement CRUD operations counts
     if (countsST) {

From f5b70935ecb75e589136e4f7a5daf54cb7d52dbd Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 22 Nov 2024 10:08:56 -0800
Subject: [PATCH 05/29] Add support for deleteDeprecated option in civic

---
 src/civic/index.js | 28 +++++++++++++++++++++-------
 1 file changed, 21 insertions(+), 7 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index f5611ec6..a6640f0a 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -19,6 +19,7 @@ const {
     contentMatching,
     createStatement,
     deleteStatements,
+    getStatements,
     needsUpdate,
     updateStatement,
 } = require('./statement');
@@ -55,6 +56,7 @@ const incrementCounts = (initial, updates) => {
  *
  * @param {object} param0
  * @param {ApiConnection} param0.conn the api connection object for GraphKB
+ * @param {?boolean} param0.deleteDeprecated deletion of existing GraphKB Statements related to deprecated evidence(s)
  * @param {string} param0.errorLogPrefix prefix to the generated error json file
  * @param {number} param0.maxRecords limit of EvidenceItem records to be processed and upload
  * @param {?boolean} param0.noDeleteOnUnmatched no deletion of existing GraphKB Statements related to unmatched combination(s)
@@ -64,6 +66,7 @@ const incrementCounts = (initial, updates) => {
  */
 const upload = async ({
     conn,
+    deleteDeprecated = false, // Won't delete deprecated sourceIds by default
     errorLogPrefix,
     maxRecords,
     noDeleteOnUnmatched = false,
@@ -421,22 +424,32 @@ const upload = async ({
     }
 
     // DELETING UNWANTED GRAPHKB STATEMENTS
-    // sourceIds no longer in CIViC (not accepted/submitted by trustedCurators) but still in GraphKB
+    // sourceIds no longer in CIViC (not accepted/submitted-by-trustedCurators) but still in GraphKB
     const allIdsFromCivic = new Set(evidenceItems.map(r => r.id.toString()));
-    const toDelete = new Set([...sourceIdsFromGKB].filter(x => !allIdsFromCivic.has(x)));
+    const sourceIdstoDeleteStatementsFrom = Array.from(
+        new Set([...sourceIdsFromGKB].filter(x => !allIdsFromCivic.has(x)))
+    );
     logger.info();
     logger.info('***** Deprecated items *****');
-    logger.warn(`${toDelete.size} deprecated ${SOURCE_DEFN.name} Evidence Items still in GraphKB Statement`);
+    logger.warn(`${sourceIdstoDeleteStatementsFrom.length} deprecated ${SOURCE_DEFN.name} Evidence Items still in GraphKB Statement`);
 
-    if (toDelete.size > 0) {
-        logger.info(`sourceIds: ${Array.from(toDelete)}`);
+    if (sourceIdstoDeleteStatementsFrom.length > 0) {
+        logger.info(`sourceIds: ${sourceIdstoDeleteStatementsFrom}`);
     }
 
     // GraphKB Statements Soft-deletion
-    if (!noUpdate && toDelete.size > 0) {
+    if (sourceIdstoDeleteStatementsFrom.length > 0) {
+        if (!deleteDeprecated) {
+            // Do not delete any statements if no deleteDeprecated flag
+            const deprecatedStatementRids = await getStatements(conn, { source: sourceRid, sourceIds: sourceIdstoDeleteStatementsFrom});
+            logger.warn(`${deprecatedStatementRids.length} corresponding deprecated statement(s). To be reviewed since no deleteDeprecated flag`);    
+            const deprecatedStatementsFilepath = `${errorLogPrefix}-civic-deprecatedStatements.json`;
+            logger.info(`writing ${deprecatedStatementsFilepath}`);
+            fs.writeFileSync(deprecatedStatementsFilepath, JSON.stringify(deprecatedStatementRids, null, 2));
+        } else {
         const deletedCount = await deleteStatements(conn, {
             source: sourceRid,
-            sourceIds: Array.from(toDelete),
+                sourceIds: sourceIdstoDeleteStatementsFrom,
         });
         const attempts = deletedCount.success + deletedCount.err;
         logger.info(`${deletedCount.success}/${attempts} soft-deleted statements`);
@@ -446,6 +459,7 @@ const upload = async ({
             countsST.delete.success += deletedCount.success;
         } else {
             countsST = { delete: { err: deletedCount.err, success: deletedCount.success } };
+            }
         }
     }
 

From 8aa00c4a7c6c51d2b0d86238e6f857330ca76caf Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 22 Nov 2024 11:38:40 -0800
Subject: [PATCH 06/29] Fix linting

---
 src/civic/evidenceItem.js |  2 +-
 src/civic/index.js        | 50 ++++++++++++++++++++++-----------------
 src/civic/variant.js      |  4 ++--
 3 files changed, 31 insertions(+), 25 deletions(-)

diff --git a/src/civic/evidenceItem.js b/src/civic/evidenceItem.js
index 0f49505a..2178cb39 100644
--- a/src/civic/evidenceItem.js
+++ b/src/civic/evidenceItem.js
@@ -180,7 +180,7 @@ const processCombination = async (conn, {
             const processedVariants = await processVariantRecord(conn, variant, feature);
             logger.verbose(`converted variant name (${variant.name}) to variants (${processedVariants.map(v => v.displayName).join(', and ')})`);
             variants.push(...processedVariants);
-        } catch {
+        } catch (err) {
             throw new Error(`unable to process the variant (id=${variant.id}, name=${variant.name})`);
         }
     }
diff --git a/src/civic/index.js b/src/civic/index.js
index a6640f0a..262e1d2a 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -186,8 +186,8 @@ const upload = async ({
         processingIntoCombinations: new Map(),
         relevance: new Map(),
     };
-    const statementsToReview_unmatched_processingError = new Map();
-    const statementsToReview_unmatched = new Map();
+    const statementsToReviewUnmatchedProcessingError = new Map();
+    const statementsToReviewUnmatched = new Map();
 
     logger.info(`\n\n${'#'.repeat(80)}\n## PROCESSING RECORDS\n${'#'.repeat(80)}\n`);
     let recordNumber = 0;
@@ -378,11 +378,11 @@ const upload = async ({
             if (processCombinationErrors > 0) {
                 // Do not delete any statements if some combinations have processing errors
                 logger.warn(`${toDelete.length} unmatched statement(s). To be reviewed since some processing errors occured`);
-                statementsToReview_unmatched_processingError.set(id, rids);
+                statementsToReviewUnmatchedProcessingError.set(id, rids);
             } else if (noDeleteOnUnmatched) {
                 // Do not delete any statements if noDeleteOnUnmatched flag
                 logger.warn(`${toDelete.length} unmatched statement(s). To be reviewed since the noDeleteOnUnmatched flag is being used`);
-                statementsToReview_unmatched.set(id, rids);
+                statementsToReviewUnmatched.set(id, rids);
             } else {
                 loaclCountsST.delete = await deleteStatements(conn, { rids });
             }
@@ -427,7 +427,7 @@ const upload = async ({
     // sourceIds no longer in CIViC (not accepted/submitted-by-trustedCurators) but still in GraphKB
     const allIdsFromCivic = new Set(evidenceItems.map(r => r.id.toString()));
     const sourceIdstoDeleteStatementsFrom = Array.from(
-        new Set([...sourceIdsFromGKB].filter(x => !allIdsFromCivic.has(x)))
+        new Set([...sourceIdsFromGKB].filter(x => !allIdsFromCivic.has(x))),
     );
     logger.info();
     logger.info('***** Deprecated items *****');
@@ -441,24 +441,30 @@ const upload = async ({
     if (sourceIdstoDeleteStatementsFrom.length > 0) {
         if (!deleteDeprecated) {
             // Do not delete any statements if no deleteDeprecated flag
-            const deprecatedStatementRids = await getStatements(conn, { source: sourceRid, sourceIds: sourceIdstoDeleteStatementsFrom});
-            logger.warn(`${deprecatedStatementRids.length} corresponding deprecated statement(s). To be reviewed since no deleteDeprecated flag`);    
+            const deprecatedStatementRids = await getStatements(
+                conn,
+                { source: sourceRid, sourceIds: sourceIdstoDeleteStatementsFrom },
+            );
+            logger.warn(`${deprecatedStatementRids.length} corresponding deprecated statement(s). To be reviewed since no deleteDeprecated flag`);
             const deprecatedStatementsFilepath = `${errorLogPrefix}-civic-deprecatedStatements.json`;
             logger.info(`writing ${deprecatedStatementsFilepath}`);
-            fs.writeFileSync(deprecatedStatementsFilepath, JSON.stringify(deprecatedStatementRids, null, 2));
+            fs.writeFileSync(
+                deprecatedStatementsFilepath,
+                JSON.stringify(deprecatedStatementRids, null, 2),
+            );
         } else {
-        const deletedCount = await deleteStatements(conn, {
-            source: sourceRid,
+            const deletedCount = await deleteStatements(conn, {
+                source: sourceRid,
                 sourceIds: sourceIdstoDeleteStatementsFrom,
-        });
-        const attempts = deletedCount.success + deletedCount.err;
-        logger.info(`${deletedCount.success}/${attempts} soft-deleted statements`);
+            });
+            const attempts = deletedCount.success + deletedCount.err;
+            logger.info(`${deletedCount.success}/${attempts} soft-deleted statements`);
 
-        if (countsST) {
-            countsST.delete.err += deletedCount.err;
-            countsST.delete.success += deletedCount.success;
-        } else {
-            countsST = { delete: { err: deletedCount.err, success: deletedCount.success } };
+            if (countsST) {
+                countsST.delete.err += deletedCount.err;
+                countsST.delete.success += deletedCount.success;
+            } else {
+                countsST = { delete: { err: deletedCount.err, success: deletedCount.success } };
             }
         }
     }
@@ -467,10 +473,10 @@ const upload = async ({
     // so a reviewer can decide if corresponding statements need to be deleted or not
     logger.info();
     logger.info('***** Unmatched cases to be reviewed for deletion *****');
-    logger.warn(`${statementsToReview_unmatched_processingError.size} Evidence Item(s) with processing errors leading to unmatched Statement(s)`);
-    statementsToReview_unmatched_processingError.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
-    logger.warn(`${statementsToReview_unmatched.size} Evidence Item(s) with unmatched Statement(s) with no processing error involved`);
-    statementsToReview_unmatched.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
+    logger.warn(`${statementsToReviewUnmatchedProcessingError.size} Evidence Item(s) with processing errors leading to unmatched Statement(s)`);
+    statementsToReviewUnmatchedProcessingError.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
+    logger.warn(`${statementsToReviewUnmatched.size} Evidence Item(s) with unmatched Statement(s) with no processing error involved`);
+    statementsToReviewUnmatched.forEach((v, k) => logger.info(`${k} -> ${JSON.stringify(v)}`));
 
     // Logging Statement CRUD operations counts
     if (countsST) {
diff --git a/src/civic/variant.js b/src/civic/variant.js
index f66c011b..c916976e 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -275,7 +275,7 @@ const uploadNormalizedVariant = async (conn, normalizedVariant, feature) => {
         } catch (err) {
             try {
                 variantType = await conn.getVocabularyTerm(normalizedVariant.type || content.type);
-            } catch {
+            } catch (e) {
                 throw new Error(`Unable to upload CIVIC variant (${normalizedVariant}})`);
             }
         }
@@ -396,7 +396,7 @@ const processVariantRecord = async (conn, civicVariantRecord, feature) => {
         }
     } catch (err) {
         VARIANT_CACHE.set(JSON.stringify(rawVariant), { err });
-        throw err
+        throw err;
     }
 
     VARIANT_CACHE.set(JSON.stringify(rawVariant), { result });

From 933aa23dd92a6881809ce4ceeb1b1d9dcbf7d6f0 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 10:15:20 -0800
Subject: [PATCH 07/29] Fix error msg in util.js::requestWithRetry()

---
 src/util.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/util.js b/src/util.js
index 45c492ab..0a4a6823 100644
--- a/src/util.js
+++ b/src/util.js
@@ -175,7 +175,7 @@ const requestWithRetry = async (requestOpt, { waitSeconds = 2, retries = 1, useC
     } catch (err) {
         if (err.statusCode === HTTP_STATUS_CODES.TOO_MANY_REQUESTS && retries > 0) {
             await sleep(waitSeconds);
-            logger.warn(`TIMEOUT, retrying request ${requestOpt.url}`);
+            logger.warn(`TIMEOUT, retrying request ${requestOpt.uri} ${JSON.stringify(requestOpt.qs)}`);
             return requestWithRetry(requestOpt, { retries: retries - 1, waitSeconds });
         }
         throw err;

From 248f7f796bd4224dc5a863462d2d3f2575caf4c8 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 10:49:28 -0800
Subject: [PATCH 08/29] Update parser to v2.1.1 and add toJSON() method

---
 package-lock.json                    | 76 +++++++++++++++++-----------
 package.json                         |  2 +-
 src/PMC4232638/index.js              |  7 ++-
 src/cancergenomeinterpreter/index.js | 13 +++--
 src/cancerhotspots/index.js          | 11 ++--
 src/cgl/index.js                     |  8 +--
 src/civic/evidenceItem.js            |  2 +-
 src/civic/profile.js                 |  2 +-
 src/civic/publication.js             |  2 +-
 src/civic/relevance.js               |  2 +-
 src/civic/variant.js                 | 18 ++++---
 src/cosmic/resistance.js             | 11 ++--
 src/docm/index.js                    |  9 ++--
 src/entrez/snp.js                    | 11 ++--
 src/moa/index.js                     | 15 +++---
 src/oncokb/index.js                  | 17 ++++---
 src/util.js                          | 44 ++++++++++++++++
 src/variants/index.js                |  7 ++-
 18 files changed, 174 insertions(+), 83 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 674875bd..4e380348 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -9,7 +9,7 @@
       "version": "8.0.2",
       "license": "GPL-3",
       "dependencies": {
-        "@bcgsc-pori/graphkb-parser": "^1.1.1",
+        "@bcgsc-pori/graphkb-parser": "^2.1.0",
         "@bcgsc-pori/graphkb-schema": "^3.14.3",
         "ajv": "^6.10.0",
         "argparse": "^2.0.1",
@@ -609,9 +609,9 @@
       }
     },
     "node_modules/@bcgsc-pori/graphkb-parser": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-1.1.1.tgz",
-      "integrity": "sha512-xh6hl+FQpAY9evB1O9hsG5LLr7bP1z1uOA4zVCsyJ0WUPTc7+NST1zGOSDGCLolJeq/mI4x4UeTaShKjSGxwhw==",
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-2.1.0.tgz",
+      "integrity": "sha512-EIVRjRdqJv7RjtvZ+wK3qQDLORPAuKoqFkGUg/pHU3JnpgQMXgeOEHBfuwh6U+P09oY1TQdspS7+vUjpINapBg==",
       "dependencies": {
         "json-cycle": "^1.3.0"
       }
@@ -631,6 +631,14 @@
         "@bcgsc-pori/graphkb-parser": ">=1.0.0 <2.0.0"
       }
     },
+    "node_modules/@bcgsc-pori/graphkb-schema/node_modules/@bcgsc-pori/graphkb-parser": {
+      "version": "1.1.3",
+      "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-1.1.3.tgz",
+      "integrity": "sha512-qy86oMsygnWlS5oEONpMSI96XcIgK8//RvYfYxA/6Yy0XuDbbTG9YF6lqyylT9YPiAfpQau5QZTAWEPCpPD5jA==",
+      "dependencies": {
+        "json-cycle": "^1.3.0"
+      }
+    },
     "node_modules/@bcoe/v8-coverage": {
       "version": "0.2.3",
       "resolved": "https://registry.npmjs.org/@bcoe/v8-coverage/-/v8-coverage-0.2.3.tgz",
@@ -3127,9 +3135,9 @@
       }
     },
     "node_modules/cross-spawn": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
-      "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==",
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
+      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
       "dev": true,
       "dependencies": {
         "path-key": "^3.1.0",
@@ -9873,13 +9881,13 @@
       "dev": true
     },
     "node_modules/micromatch": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.4.tgz",
-      "integrity": "sha512-pRmzw/XUcwXGpD9aI9q/0XOwLNygjETJ8y0ao0wdqprrzDa4YnxLcz7fQRZr8voh8V10kGhABbNcHVk5wHgWwg==",
+      "version": "4.0.8",
+      "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.8.tgz",
+      "integrity": "sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA==",
       "dev": true,
       "dependencies": {
-        "braces": "^3.0.1",
-        "picomatch": "^2.2.3"
+        "braces": "^3.0.3",
+        "picomatch": "^2.3.1"
       },
       "engines": {
         "node": ">=8.6"
@@ -10330,9 +10338,9 @@
       "dev": true
     },
     "node_modules/picomatch": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-2.3.0.tgz",
-      "integrity": "sha512-lY1Q/PiJGC2zOv/z391WOTD+Z02bCgsFfvxoXXf6h7kv9o+WmsmzYqrAwY63sNgOxE4xEdq0WyUnXfKeBrSvYw==",
+      "version": "2.3.1",
+      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-2.3.1.tgz",
+      "integrity": "sha512-JU3teHTNjmE2VCGFzuY8EXzCDVwEqB2a8fsIvwaStHhAWJEeVd1o1QD80CU6+ZdEXXSLbSsuLwJjkCBWqRQUVA==",
       "dev": true,
       "engines": {
         "node": ">=8.6"
@@ -12219,9 +12227,9 @@
       }
     },
     "@bcgsc-pori/graphkb-parser": {
-      "version": "1.1.1",
-      "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-1.1.1.tgz",
-      "integrity": "sha512-xh6hl+FQpAY9evB1O9hsG5LLr7bP1z1uOA4zVCsyJ0WUPTc7+NST1zGOSDGCLolJeq/mI4x4UeTaShKjSGxwhw==",
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-2.1.0.tgz",
+      "integrity": "sha512-EIVRjRdqJv7RjtvZ+wK3qQDLORPAuKoqFkGUg/pHU3JnpgQMXgeOEHBfuwh6U+P09oY1TQdspS7+vUjpINapBg==",
       "requires": {
         "json-cycle": "^1.3.0"
       }
@@ -12236,6 +12244,16 @@
         "lodash.omit": "4.5.0",
         "uuid": "3.3.2",
         "uuid-validate": "0.0.3"
+      },
+      "dependencies": {
+        "@bcgsc-pori/graphkb-parser": {
+          "version": "1.1.3",
+          "resolved": "https://registry.npmjs.org/@bcgsc-pori/graphkb-parser/-/graphkb-parser-1.1.3.tgz",
+          "integrity": "sha512-qy86oMsygnWlS5oEONpMSI96XcIgK8//RvYfYxA/6Yy0XuDbbTG9YF6lqyylT9YPiAfpQau5QZTAWEPCpPD5jA==",
+          "requires": {
+            "json-cycle": "^1.3.0"
+          }
+        }
       }
     },
     "@bcoe/v8-coverage": {
@@ -14225,9 +14243,9 @@
       }
     },
     "cross-spawn": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.3.tgz",
-      "integrity": "sha512-iRDPJKUPVEND7dHPO8rkbOnPpyDygcDFtWjpeWNCgy8WP2rXcxXL8TskReQl6OrB2G7+UJrags1q15Fudc7G6w==",
+      "version": "7.0.6",
+      "resolved": "https://registry.npmjs.org/cross-spawn/-/cross-spawn-7.0.6.tgz",
+      "integrity": "sha512-uV2QOWP2nWzsy2aMp8aRibhi9dlzF5Hgh5SHaB9OiTGEyDTiJJyx0uy51QXdyWbtAHNua4XJzUKca3OzKUd3vA==",
       "dev": true,
       "requires": {
         "path-key": "^3.1.0",
@@ -19421,13 +19439,13 @@
       "dev": true
     },
     "micromatch": {
-      "version": "4.0.4",
-      "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.4.tgz",
-      "integrity": "sha512-pRmzw/XUcwXGpD9aI9q/0XOwLNygjETJ8y0ao0wdqprrzDa4YnxLcz7fQRZr8voh8V10kGhABbNcHVk5wHgWwg==",
+      "version": "4.0.8",
+      "resolved": "https://registry.npmjs.org/micromatch/-/micromatch-4.0.8.tgz",
+      "integrity": "sha512-PXwfBhYu0hBCPw8Dn0E+WDYb7af3dSLVWKi3HGv84IdF4TyFoC0ysxFd0Goxw7nSv4T/PzEJQxsYsEiFCKo2BA==",
       "dev": true,
       "requires": {
-        "braces": "^3.0.1",
-        "picomatch": "^2.2.3"
+        "braces": "^3.0.3",
+        "picomatch": "^2.3.1"
       }
     },
     "mime-db": {
@@ -19776,9 +19794,9 @@
       "dev": true
     },
     "picomatch": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-2.3.0.tgz",
-      "integrity": "sha512-lY1Q/PiJGC2zOv/z391WOTD+Z02bCgsFfvxoXXf6h7kv9o+WmsmzYqrAwY63sNgOxE4xEdq0WyUnXfKeBrSvYw==",
+      "version": "2.3.1",
+      "resolved": "https://registry.npmjs.org/picomatch/-/picomatch-2.3.1.tgz",
+      "integrity": "sha512-JU3teHTNjmE2VCGFzuY8EXzCDVwEqB2a8fsIvwaStHhAWJEeVd1o1QD80CU6+ZdEXXSLbSsuLwJjkCBWqRQUVA==",
       "dev": true
     },
     "pirates": {
diff --git a/package.json b/package.json
index b4b59389..4ef77ca7 100644
--- a/package.json
+++ b/package.json
@@ -12,7 +12,7 @@
   "private": true,
   "license": "GPL-3",
   "dependencies": {
-    "@bcgsc-pori/graphkb-parser": "^1.1.1",
+    "@bcgsc-pori/graphkb-parser": "^2.1.0",
     "@bcgsc-pori/graphkb-schema": "^3.14.3",
     "ajv": "^6.10.0",
     "argparse": "^2.0.1",
diff --git a/src/PMC4232638/index.js b/src/PMC4232638/index.js
index 1f69050b..5334b3b8 100644
--- a/src/PMC4232638/index.js
+++ b/src/PMC4232638/index.js
@@ -1,12 +1,15 @@
 const readXlsxFile = require('read-excel-file/node');
-const kbParser = require('@bcgsc-pori/graphkb-parser');
 
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
 const { logger } = require('../logging');
 const { rid } = require('../graphkb');
 const _pubmed = require('../entrez/pubmed');
 const _entrezGene = require('../entrez/gene');
 const { PMC4232638: SOURCE_DEFN } = require('../sources');
 
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const TP53_COLS = {
     DOM: 'Functional categories for TP53 - Dominant negative activity',
@@ -134,7 +137,7 @@ const uploadFile = async ({ conn, filename }) => {
         logger.info(`loading: ${row.Gene}:${row['Amino acid change']}`);
 
         try {
-            const parsed = kbParser.variant.parse(`p.${row['Amino acid change']}`, false).toJSON();
+            const parsed = parseVariant(`p.${row['Amino acid change']}`, false).toJSON();
             const [gene] = await _entrezGene.fetchAndLoadBySymbol(conn, row.Gene);
             const relevance = await conn.getVocabularyTerm(row.relevance);
             const evidence = await _pubmed.fetchAndLoadByIds(conn, row.evidence);
diff --git a/src/cancergenomeinterpreter/index.js b/src/cancergenomeinterpreter/index.js
index 2c69dd42..d07638fa 100644
--- a/src/cancergenomeinterpreter/index.js
+++ b/src/cancergenomeinterpreter/index.js
@@ -1,6 +1,9 @@
 const fs = require('fs');
 
-const kbParser = require('@bcgsc-pori/graphkb-parser');
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const {
     loadDelimToJson,
@@ -217,7 +220,7 @@ const processVariants = async ({ conn, row, source }) => {
     }
 
     if (genomic && !isCat) {
-        const parsed = kbParser.variant.parse(genomic).toJSON();
+        const parsed = parseVariant(genomic).toJSON();
         const reference1 = await conn.getUniqueRecordBy({
             filters: {
                 AND: [
@@ -242,7 +245,7 @@ const processVariants = async ({ conn, row, source }) => {
     }
 
     if (protein && !isCat) {
-        const parsed = kbParser.variant.parse(`${gene}:${protein.split(':')[1]}`).toJSON();
+        const parsed = parseVariant(`${gene}:${protein.split(':')[1]}`).toJSON();
         const type = await conn.getVocabularyTerm(parsed.type);
         proteinVariant = await conn.addVariant({
             content: { ...parsed, reference1: rid(gene1Record), type },
@@ -251,7 +254,7 @@ const processVariants = async ({ conn, row, source }) => {
         });
     }
     if (transcript && cds && !isCat) {
-        const parsed = kbParser.variant.parse(`${transcript}:${cds}`).toJSON();
+        const parsed = parseVariant(`${transcript}:${cds}`).toJSON();
         const reference1 = await conn.getUniqueRecordBy({
             filters: { AND: [{ biotype: 'transcript' }, { sourceId: transcript }, { sourceIdVersion: null }] },
             sort: orderPreferredOntologyTerms,
@@ -265,7 +268,7 @@ const processVariants = async ({ conn, row, source }) => {
         });
     }
     if (exonic && !isCat) {
-        const parsed = kbParser.variant.parse(`${gene}:${exonic}`).toJSON();
+        const parsed = parseVariant(`${gene}:${exonic}`).toJSON();
         const type = await conn.getVocabularyTerm(parsed.type);
         exonicVariant = await conn.addVariant({
             content: { ...parsed, reference1: rid(gene1Record), type },
diff --git a/src/cancerhotspots/index.js b/src/cancerhotspots/index.js
index 9225c4b8..e048be4b 100644
--- a/src/cancerhotspots/index.js
+++ b/src/cancerhotspots/index.js
@@ -5,7 +5,10 @@ const fs = require('fs');
 
 const csv = require('fast-csv');
 
-const { variant: { parse: variantParser } } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const {
     convertRowFields,
@@ -101,7 +104,7 @@ const processVariants = async ({ conn, record, source }) => {
             // deletion
             notation = `${notation}${start}_${stop}del${refSeq}`;
         }
-        const variant = variantParser(notation).toJSON();
+        const variant = parseVariant(notation).toJSON();
 
         variant.reference1 = rid(reference1);
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
@@ -125,7 +128,7 @@ const processVariants = async ({ conn, record, source }) => {
             [reference1] = await _entrezGene.fetchAndLoadByIds(conn, [geneId]);
             featureCache[geneId] = reference1;
         }
-        const variant = variantParser(
+        const variant = parseVariant(
             protein.replace(/fs\*\?$/, 'fs'), // ignore uncertain truncations
             false,
         ).toJSON();
@@ -163,7 +166,7 @@ const processVariants = async ({ conn, record, source }) => {
             featureCache[transcriptId] = reference1;
         }
         // parse the cds variant
-        const variant = variantParser(cds, false).toJSON();
+        const variant = parseVariant(cds, false).toJSON();
 
         variant.reference1 = reference1;
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
diff --git a/src/cgl/index.js b/src/cgl/index.js
index cac1b51f..56cca0d5 100644
--- a/src/cgl/index.js
+++ b/src/cgl/index.js
@@ -1,6 +1,6 @@
 const fs = require('fs');
 
-const { variant: { parse: variantParser } } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     loadDelimToJson,
@@ -46,7 +46,7 @@ const loadCdsVariant = async (graphkbConn, transcriptId, cdsNotation) => {
     // add the cds variant
     const {
         noFeatures, multiFeature, prefix, ...variant
-    } = variantParser(cdsNotation, false);
+    } = parseVariant(cdsNotation, false);
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const cds = rid(await graphkbConn.addVariant({
@@ -87,7 +87,7 @@ const loadProteinVariant = async (graphkbConn, gene, proteinNotation) => {
     // add the cds variant
     const {
         noFeatures, multiFeature, prefix, ...variant
-    } = variantParser(proteinNotation, false);
+    } = parseVariant(proteinNotation, false);
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const protein = rid(await graphkbConn.addVariant({
@@ -163,7 +163,7 @@ const loadGenomicVariant = async (graphkbConn, chromosome, position, ref, alt) =
     // add the cds variant
     const {
         noFeatures, multiFeature, prefix, ...variant
-    } = variantParser(notation, false);
+    } = parseVariant(notation, false);
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const genomic = rid(await graphkbConn.addVariant({
diff --git a/src/civic/evidenceItem.js b/src/civic/evidenceItem.js
index 2178cb39..e54619e9 100644
--- a/src/civic/evidenceItem.js
+++ b/src/civic/evidenceItem.js
@@ -3,7 +3,7 @@ const path = require('path');
 
 const _ = require('lodash');
 const Ajv = require('ajv');
-const { error: { ErrorMixin } } = require('@bcgsc-pori/graphkb-parser');
+const { ErrorMixin } = require('@bcgsc-pori/graphkb-parser');
 
 const { checkSpec, request } = require('../util');
 const { logger } = require('../logging');
diff --git a/src/civic/profile.js b/src/civic/profile.js
index 4d6845d8..912c83b0 100644
--- a/src/civic/profile.js
+++ b/src/civic/profile.js
@@ -2,7 +2,7 @@
  * Introducing Molecular Profiles with CIViC GraphQL API v2.2.0
  * [EvidenceItem]--(many-to-one)--[MolecularProfile]--(many-to-many)--[Variant]
  */
-const { error: { ErrorMixin } } = require('@bcgsc-pori/graphkb-parser');
+const { ErrorMixin } = require('@bcgsc-pori/graphkb-parser');
 
 
 class NotImplementedError extends ErrorMixin { }
diff --git a/src/civic/publication.js b/src/civic/publication.js
index 644111ee..33e0c58e 100644
--- a/src/civic/publication.js
+++ b/src/civic/publication.js
@@ -1,4 +1,4 @@
-const { error: { ErrorMixin } } = require('@bcgsc-pori/graphkb-parser');
+const { ErrorMixin } = require('@bcgsc-pori/graphkb-parser');
 
 const _asco = require('../asco');
 const _pubmed = require('../entrez/pubmed');
diff --git a/src/civic/relevance.js b/src/civic/relevance.js
index 3c1bff1f..39a4c92c 100644
--- a/src/civic/relevance.js
+++ b/src/civic/relevance.js
@@ -1,4 +1,4 @@
-const { error: { ErrorMixin } } = require('@bcgsc-pori/graphkb-parser');
+const { ErrorMixin } = require('@bcgsc-pori/graphkb-parser');
 
 class NotImplementedError extends ErrorMixin { }
 
diff --git a/src/civic/variant.js b/src/civic/variant.js
index c916976e..78f7b223 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -1,14 +1,17 @@
-const kbParser = require('@bcgsc-pori/graphkb-parser');
+const { ErrorMixin, ParsingError, parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
 const { rid } = require('../graphkb');
 const _entrezGene = require('../entrez/gene');
 const _snp = require('../entrez/snp');
 const { civic: SOURCE_DEFN } = require('../sources');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
-const { error: { ErrorMixin, ParsingError } } = kbParser;
 class NotImplementedError extends ErrorMixin { }
 
 const VARIANT_CACHE = new Map();
 
+
 // based on discussion with cam here: https://www.bcgsc.ca/jira/browse/KBDEV-844
 const SUBS = {
     'E746_T751>I': 'E746_T751delinsI',
@@ -223,11 +226,11 @@ const normalizeVariantRecord = ({
 
     // try parser fallback for notation that is close to correct
     try {
-        kbParser.variant.parse(name, false);
+        parseVariant(name, false);
         return [{ positional: true, reference1: { ...referenceGene }, variant: name }];
     } catch (err) {
         try {
-            kbParser.variant.parse(`p.${name}`, false);
+            parseVariant(`p.${name}`, false);
             return [{
                 positional: true,
                 reference1: { ...referenceGene },
@@ -261,10 +264,9 @@ const uploadNormalizedVariant = async (conn, normalizedVariant, feature) => {
     } else {
         let content = {};
 
-        if (normalizedVariant.positional) {
-            content = kbParser.variant.parse(normalizedVariant.variant, false).toJSON();
-        }
-        let variantType;
+    if (normalizedVariant.positional) {
+        content = parseVariant(normalizedVariant.variant, false).toJSON();
+    }
 
         // try to fetch civic specific term first
         try {
diff --git a/src/cosmic/resistance.js b/src/cosmic/resistance.js
index 5ff8e29e..1570830d 100644
--- a/src/cosmic/resistance.js
+++ b/src/cosmic/resistance.js
@@ -3,7 +3,10 @@
  */
 const fs = require('fs');
 
-const { variant: { parse: variantParser } } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const {
     loadDelimToJson,
@@ -77,7 +80,7 @@ const processVariants = async ({ conn, record, source }) => {
 
     try {
         // add the protein variant with its protein translation
-        const variant = variantParser(record.protein, false).toJSON();
+        const variant = parseVariant(record.protein, false).toJSON();
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
 
         const reference1 = rid(await _ensembl.fetchAndLoadById(
@@ -113,7 +116,7 @@ const processVariants = async ({ conn, record, source }) => {
     // create the cds variant
     if (record.cds && record.cds.trim()) {
         try {
-            const variant = variantParser(record.cds, false).toJSON();
+            const variant = parseVariant(record.cds, false).toJSON();
             // get the ensembl transcript
             const reference1 = rid(await _ensembl.fetchAndLoadById(
                 conn,
@@ -143,7 +146,7 @@ const processVariants = async ({ conn, record, source }) => {
     // add the genomic representation
     if (record.genomic) {
         try {
-            const variant = variantParser(record.genomic, false).toJSON();
+            const variant = parseVariant(record.genomic, false).toJSON();
             // get the chromosome
             const reference1 = rid(await conn.getUniqueRecordBy({
                 filters: {
diff --git a/src/docm/index.js b/src/docm/index.js
index 4b7d5f60..08732105 100644
--- a/src/docm/index.js
+++ b/src/docm/index.js
@@ -6,7 +6,10 @@
 const Ajv = require('ajv');
 const fs = require('fs');
 
-const { variant: { parse: variantParser } } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const { checkSpec, request } = require('../util');
 const {
@@ -107,7 +110,7 @@ const processVariants = async ({ conn, source, record: docmRecord }) => {
     try {
         // create the protein variant
         const [reference1] = await _gene.fetchAndLoadBySymbol(conn, gene);
-        let variant = variantParser(parseDocmVariant(aminoAcid), false).toJSON();
+        let variant = parseVariant(parseDocmVariant(aminoAcid), false).toJSON();
         const type = await conn.getVocabularyTerm(variant.type);
         protein = variant = await conn.addVariant({
             content: { ...variant, reference1: rid(reference1), type: rid(type) },
@@ -121,7 +124,7 @@ const processVariants = async ({ conn, source, record: docmRecord }) => {
 
     try {
         // create the genomic variant
-        let variant = variantParser(buildGenomicVariant(docmRecord), false).toJSON();
+        let variant = parseVariant(buildGenomicVariant(docmRecord), false).toJSON();
         const type = await conn.getVocabularyTerm(variant.type);
         const reference1 = await conn.getUniqueRecordBy({
             filters: {
diff --git a/src/entrez/snp.js b/src/entrez/snp.js
index 6611913b..362ac3f4 100644
--- a/src/entrez/snp.js
+++ b/src/entrez/snp.js
@@ -1,7 +1,6 @@
 const Ajv = require('ajv');
 
-const { variant: { parse: variantParser } } = require('@bcgsc-pori/graphkb-parser');
-
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
 const { checkSpec } = require('../util');
 const {
     fetchByIdList, uploadRecord, preLoadCache: preLoadAnyCache, BASE_FETCH_URL,
@@ -11,6 +10,10 @@ const entrezGene = require('./gene');
 const { rid } = require('../graphkb');
 const { logger } = require('../logging');
 
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
+
 const ajv = new Ajv();
 
 const { dbSnp: SOURCE_DEFN } = require('../sources');
@@ -49,7 +52,7 @@ const loadFromDocsumHgvs = async (api, hgvsVariants) => {
 
     try {
         if (hgvsVariants.cds) {
-            const parsed = variantParser(hgvsVariants.cds.split('|')[0], true).toJSON();
+            const parsed = parseVariant(hgvsVariants.cds.split('|')[0], true).toJSON();
             const [transcript] = await refseq.fetchAndLoadByIds(api, [parsed.reference1]);
             const type = await api.getVocabularyTerm(parsed.type);
             cds = await api.addVariant({
@@ -65,7 +68,7 @@ const loadFromDocsumHgvs = async (api, hgvsVariants) => {
     try {
         if (hgvsVariants.protein) {
             const gene = hgvsVariants.protein.split('|').find(p => p.startsWith('GENE='));
-            const parsed = variantParser(hgvsVariants.protein.split('|')[0], true).toJSON();
+            const parsed = parseVariant(hgvsVariants.protein.split('|')[0], true).toJSON();
             const [reference1] = await refseq.fetchAndLoadByIds(api, [parsed.reference1]);
             const type = await api.getVocabularyTerm(parsed.type);
             protein = await api.addVariant({
diff --git a/src/moa/index.js b/src/moa/index.js
index 3455000e..7f314c56 100644
--- a/src/moa/index.js
+++ b/src/moa/index.js
@@ -1,6 +1,9 @@
-
 const Ajv = require('ajv');
-const kbParser = require('@bcgsc-pori/graphkb-parser');
+
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const { checkSpec, requestWithRetry } = require('../util');
 const { moa: SOURCE_DEFN } = require('../sources');
@@ -59,7 +62,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the genomic variant if we have the appropriate fields
     if (!['reference_allele', 'alternate_allele', 'start_position', 'end_position', 'chromosome'].some(v => moaVariant[v] === null)) {
-        const hgvsg = kbParser.variant.parse(composeGenomicHgvs(moaVariant), false).toJSON();
+        const hgvsg = parseVariant(composeGenomicHgvs(moaVariant), false).toJSON();
         const chromosome = await conn.getUniqueRecordBy({
             filters: {
                 AND: [
@@ -85,7 +88,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the cds variant
     if (moaVariant.cdna_change !== null && moaVariant.cdna_change !== '') {
-        const hgvsc = kbParser.variant.parse(moaVariant.cdna_change, false).toJSON();
+        const hgvsc = parseVariant(moaVariant.cdna_change, false).toJSON();
         const cdsType = rid(await conn.getVocabularyTerm(hgvsc.type));
         cdsVariant = rid(await conn.addVariant({
             content: {
@@ -98,7 +101,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the protein variant
     if (moaVariant.protein_change !== null && moaVariant.protein_change !== '') {
-        const hgvsp = kbParser.variant.parse(moaVariant.protein_change, false).toJSON();
+        const hgvsp = parseVariant(moaVariant.protein_change, false).toJSON();
         const proteinType = rid(await conn.getVocabularyTerm(hgvsp.type));
         proteinVariant = rid(await conn.addVariant({
             content: {
@@ -129,7 +132,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
         } else {
             variantType = await conn.getVocabularyTerm('mutation');
         }
-        const parsed = kbParser.variant.parse(`e.${exonNumber}mut`, false).toJSON();
+        const parsed = parseVariant(`e.${exonNumber}mut`, false).toJSON();
         exonVariant = await conn.addVariant({
             content: {
                 ...parsed,
diff --git a/src/oncokb/index.js b/src/oncokb/index.js
index 38d59129..a6498496 100644
--- a/src/oncokb/index.js
+++ b/src/oncokb/index.js
@@ -5,7 +5,10 @@ const Ajv = require('ajv');
 const fs = require('fs');
 const path = require('path');
 
-const kbParser = require('@bcgsc-pori/graphkb-parser');
+const { ParsingError, parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
 
 const {
     checkSpec,
@@ -132,7 +135,7 @@ const parseVariantName = (variantIn, { reference1 } = {}) => {
     const variant = variantIn.toLowerCase().trim();
 
     try {
-        kbParser.variant.parse(`p.${variant}`, false);
+        parseVariant(`p.${variant}`, false);
         return { type: `p.${variant}` };
     } catch (err) { }
     let match = /^([a-z])?(\d+)_([a-z])?(\d+)splice$/.exec(variant);
@@ -276,11 +279,11 @@ const processVariant = async (conn, {
 
     if (!variant) {
         try {
-            variant = kbParser.variant.parse(type, false).toJSON();
+            variant = parseVariant(type, false).toJSON();
         } catch (err) {
             try {
                 // try with adding a p prefix also
-                variant = kbParser.variant.parse(`p.${type}`, false).toJSON();
+                variant = parseVariant(`p.${type}`, false).toJSON();
             } catch (err2) { }
             logger.warn(`failed to parse the variant (${type}) for record (gene=${gene}, variant=${variantName})`);
             throw err;
@@ -303,7 +306,7 @@ const processVariant = async (conn, {
 
     // create the variant
     for (const [key, value] of Object.entries(variant)) {
-        if (value instanceof kbParser.position.Position) {
+        if (value.pos) {
             variant[key] = value.toJSON();
         }
     }
@@ -327,7 +330,7 @@ const processVariant = async (conn, {
 
         try {
             // try with adding a p prefix also
-            const parsed = kbParser.variant.parse(altVariantName, false).toJSON();
+            const parsed = parseVariant(altVariantName, false).toJSON();
             parsed.reference1 = rid(reference1);
             parsed.type = rid(await getVocabulary(conn, parsed.type));
             const altVariant = rid(await conn.addVariant({
@@ -617,7 +620,7 @@ const addEvidenceLevels = async (conn, proxy, source) => {
 
     for (let [level, desc] of Object.entries(levels)) {
         if (!/^LEVEL_[A-Z0-9]+$/.exec(level)) {
-            throw new kbParser.error.ParsingError({
+            throw new ParsingError({
                 expected: '/^LEVEL_[A-Z0-9]+$/',
                 message: `Error in parsing the level name: ${level}`,
                 observed: level,
diff --git a/src/util.js b/src/util.js
index 0a4a6823..32238712 100644
--- a/src/util.js
+++ b/src/util.js
@@ -225,6 +225,49 @@ const convertRowFields = (header, row) => {
     return result;
 };
 
+/**
+ * Decorator function to add toJSON() method to parseVariant returned object
+ * (from graphkb-parser v1 not avail. anymore in v2.1.1)
+ */
+function parseVariantDecorator(parseVariant) {
+    // Method
+    function toJSON() {
+        const positionToJSON = (position) => {
+            const json = {};
+
+            for (const [attr, value] of Object.entries(position)) {
+                if (value !== null && !['prefix', 'longRefAA'].includes(attr)) {
+                    json[attr] = value;
+                }
+            }
+            return json;
+        };
+
+        const json = {};
+        const IGNORE = ['prefix', 'multiFeature', 'noFeatures', 'notationType', 'toJSON'];
+
+        for (const [attr, value] of Object.entries(this)) {
+            if (value !== undefined && !IGNORE.includes(attr)) {
+                if (value.pos) {
+                    json[attr] = positionToJSON(value);
+                } else {
+                    json[attr] = value;
+                }
+            }
+        }
+        return json;
+    }
+
+    return function (...args) {
+        const result = parseVariant(...args);
+
+        if (!('toJSON' in result) || typeof result.toJSON !== 'function') {
+            result.toJSON = toJSON;
+        }
+        return result;
+    };
+}
+
 
 module.exports = {
     checkSpec,
@@ -235,6 +278,7 @@ module.exports = {
     loadDelimToJson,
     loadXmlToJson,
     logger,
+    parseVariantDecorator,
     parseXmlToJson,
     request,
     requestWithRetry,
diff --git a/src/variants/index.js b/src/variants/index.js
index b7966754..c2aa2a52 100644
--- a/src/variants/index.js
+++ b/src/variants/index.js
@@ -1,11 +1,14 @@
 const fs = require('fs');
 
-const { variant: { parse: parseVariant } } = require('@bcgsc-pori/graphkb-parser');
-
+const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
 const { logger } = require('../logging');
 const { orderPreferredOntologyTerms, rid } = require('../graphkb');
 const { fetchAndLoadBySymbol } = require('../entrez/gene');
 
+const { parseVariantDecorator } = require('../util');
+
+const parseVariant = parseVariantDecorator(parseVariantOriginal);
+
 
 const getEntrezGene = async (conn, name) => {
     try {

From 80b2182cb47b424096e9c4340a4b26c0b23fa0c8 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:04:57 -0800
Subject: [PATCH 09/29] Linting moa & ncit index.js

---
 src/moa/index.js  | 4 ++--
 src/ncit/index.js | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/moa/index.js b/src/moa/index.js
index 7f314c56..df50c4d1 100644
--- a/src/moa/index.js
+++ b/src/moa/index.js
@@ -264,19 +264,19 @@ const loadVariant = async (conn, moaVariant) => {
 
         try {
             signature = await conn.getUniqueRecordBy({
-                target: 'Signature',
                 filters: {
                     AND: [
                         {
                             source: {
-                                target: 'Source',
                                 filters: { name: 'cosmic' },
+                                target: 'Source',
                             },
                         },
                         { sourceId: moaVariant.cosmic_signature },
                         { sourceIdVersion: '3' },
                     ],
                 },
+                target: 'Signature',
             });
         } catch (err) {
             // Enforcing usage of v3 Cosmic signatures
diff --git a/src/ncit/index.js b/src/ncit/index.js
index a85a2411..807c110d 100644
--- a/src/ncit/index.js
+++ b/src/ncit/index.js
@@ -180,8 +180,8 @@ const cleanRawRow = (rawRow) => {
             : `${row.name} [${sourceId}]`,
         endpoint,
         name: row.name.toLowerCase(),
-        sourceId,
         original_synonyms: row.synonyms,
+        sourceId,
         synonyms: Array.from(new Set(row.synonyms))
             .map(s => s.toLowerCase())
             .filter(s => s !== row.name.toLowerCase()),

From a807e82adb14062287c44f4206ae27c03775cd74 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:06:02 -0800
Subject: [PATCH 10/29] Update civic specs validation

---
 src/civic/specs.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/civic/specs.json b/src/civic/specs.json
index 740e28cc..9fc1a3db 100644
--- a/src/civic/specs.json
+++ b/src/civic/specs.json
@@ -118,7 +118,7 @@
                                                 "__typename": {
                                                     "type": "string"
                                                 },
-                                                "entrezId": {
+                                                "id": {
                                                     "type": "number"
                                                 },
                                                 "name": {
@@ -127,7 +127,7 @@
                                             },
                                             "required":[
                                                 "__typename",
-                                                "entrezId",
+                                                "id",
                                                 "name"
                                             ],
                                             "type": "object"

From 85632e4fcfb6834f50ffedebce4032c3b015f4fc Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:06:52 -0800
Subject: [PATCH 11/29] Update civic graphql query for factor & fusion

---
 src/civic/evidenceItems.graphql | 20 +++++++++++++++++++-
 1 file changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/civic/evidenceItems.graphql b/src/civic/evidenceItems.graphql
index 2d98ddbd..e9dca1d5 100644
--- a/src/civic/evidenceItems.graphql
+++ b/src/civic/evidenceItems.graphql
@@ -81,9 +81,27 @@ query evidenceItems(
           feature {
             featureInstance {
               __typename
-              ... on Factor { id }
+              ... on Factor {
+                id
+                name
+              }
+              ... on Fusion {
+                fivePrimeGene {
+                  entrezId
+                  id
+                  name
+                }
+                id
+                name
+                threePrimeGene {
+                  entrezId
+                  id
+                  name
+                }
+              }
               ... on Gene {
                 entrezId
+                id
                 name
               }
             }

From 8d9ae69e937e2f6afb5d0370b55ee032758439e4 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:09:03 -0800
Subject: [PATCH 12/29] Refactoring normalization and upload of civic variants

---
 src/civic/evidenceItem.js |  57 ++---
 src/civic/variant.js      | 467 +++++++++++++++++++++++++++-----------
 2 files changed, 356 insertions(+), 168 deletions(-)

diff --git a/src/civic/evidenceItem.js b/src/civic/evidenceItem.js
index e54619e9..81d68780 100644
--- a/src/civic/evidenceItem.js
+++ b/src/civic/evidenceItem.js
@@ -3,21 +3,17 @@ const path = require('path');
 
 const _ = require('lodash');
 const Ajv = require('ajv');
-const { ErrorMixin } = require('@bcgsc-pori/graphkb-parser');
 
 const { checkSpec, request } = require('../util');
 const { logger } = require('../logging');
 const { civic: SOURCE_DEFN } = require('../sources');
 const { EvidenceItem: evidenceSpec } = require('./specs.json');
-const _entrezGene = require('../entrez/gene');
-const { processVariantRecord } = require('./variant');
+const { normalizeVariant, uploadVariants } = require('./variant');
 const { processMolecularProfile } = require('./profile');
 const { addOrFetchTherapy, resolveTherapies } = require('./therapy');
 const { rid } = require('../graphkb');
 
 
-class NotImplementedError extends ErrorMixin { }
-
 // Spec compiler
 const ajv = new Ajv();
 const validateEvidenceSpec = ajv.compile(evidenceSpec);
@@ -114,6 +110,7 @@ const downloadEvidenceItems = async (url, trustedCurators) => {
     return { errors, records: validatedRecords };
 };
 
+
 /**
  * Format one combination from a CIViC EvidenceItem into an object
  * ready to be compared with a corresponding GraphKB statement
@@ -150,40 +147,18 @@ const processCombination = async (conn, {
     }
 
     // VARIANTS
-    // Note: the combination can have more than 1 variant
-    // if the Molecular profile was using AND operators
+    // The combination can have 1 or more CIViC variant(s),
+    // each of which can be normalized into 1 or more GraphKB variant(s).
     const { variants: civicVariants } = rawRecord;
-    const variants = [];
-
-    for (const variant of civicVariants) {
-        // Variant's Feature
-        const { feature: { featureInstance } } = variant;
-
-        // TODO: Deal with __typename === 'Factor'. No actual case as April 22nd, 2024
-        if (featureInstance.__typename !== 'Gene') {
-            throw new NotImplementedError(
-                'unable to process variant\'s feature of type other than Gene (e.g. Factor)',
-            );
-        }
+    const normalizedVariants = [];
+    const uploadedVariants = [];
 
-        let feature;
-
-        try {
-            [feature] = await _entrezGene.fetchAndLoadByIds(conn, [featureInstance.entrezId]);
-        } catch (err) {
-            logger.error(`failed to fetch variant's feature: ${featureInstance.entrezId}`);
-            throw err;
-        }
-
-        // Variant
-        try {
-            const processedVariants = await processVariantRecord(conn, variant, feature);
-            logger.verbose(`converted variant name (${variant.name}) to variants (${processedVariants.map(v => v.displayName).join(', and ')})`);
-            variants.push(...processedVariants);
-        } catch (err) {
-            throw new Error(`unable to process the variant (id=${variant.id}, name=${variant.name})`);
-        }
+    // Normalize
+    for (const record of civicVariants) {
+        normalizedVariants.push(...await normalizeVariant(record));
     }
+    // Upload
+    uploadedVariants.push(...await uploadVariants(conn, normalizedVariants));
 
     /*
         FORMATTING CONTENT FOR GRAPHKB STATEMENT
@@ -220,12 +195,12 @@ const processCombination = async (conn, {
 
     // Adding feature (reference1) or Variant (1st variant as the default) as subject.
     if (rawRecord.evidenceType === 'FUNCTIONAL') {
-        content.subject = rid(variants[0].reference1);
+        content.subject = rid(uploadedVariants[0].reference1);
     }
     if (rawRecord.evidenceType === 'ONCOGENIC') {
-        content.subject = variants.length === 1
-            ? rid(variants[0])
-            : rid(variants[0].reference1);
+        content.subject = uploadedVariants.length === 1
+            ? rid(uploadedVariants[0])
+            : rid(uploadedVariants[0].reference1);
     }
 
     // Checking for Subject
@@ -235,7 +210,7 @@ const processCombination = async (conn, {
 
     // CONDITIONS
     // Adding variants as conditions
-    content.conditions = [...variants.map(v => rid(v))];
+    content.conditions = [...uploadedVariants.map(v => rid(v))];
 
     // Adding Disease as condition
     if (content.disease) {
diff --git a/src/civic/variant.js b/src/civic/variant.js
index 78f7b223..346a3a23 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -3,6 +3,8 @@ const { rid } = require('../graphkb');
 const _entrezGene = require('../entrez/gene');
 const _snp = require('../entrez/snp');
 const { civic: SOURCE_DEFN } = require('../sources');
+const { logger } = require('../logging');
+
 const { parseVariantDecorator } = require('../util');
 
 const parseVariant = parseVariantDecorator(parseVariantOriginal);
@@ -52,20 +54,31 @@ const compareGeneNames = (gene1, gene2) => {
 };
 
 /**
- * Given a CIViC Variant record entrez information and name,
- * normalize into a set of graphkb-style variants
+ * Normalize CIViC Gene Variant record as GraphKB positional and/or category variant(s)
  *
  * @param {object} param0
  * @param {string} param0.name
  * @param {string} param0.entrezId
  * @param {string} param0.entrezName
- * @returns {object}
+ * @returns {object[]}
  */
-const normalizeVariantRecord = ({
+const normalizeGeneVariant = ({
     name: rawName, entrezId, entrezName: rawEntrezName,
 }) => {
-    const entrezName = rawEntrezName.toLowerCase().trim();
+    // Exceptions: unsupported/unimplemented CIViC variant nomenclature
+    if ([
+        'Non-V600',
+        'P-Loop Mutation',
+    ].includes(rawName)) {
+        throw new NotImplementedError(
+            `unable to process CIViC variant ${rawEntrezName} ${rawName}`,
+        );
+    }
+
+    // Substitutions: harcoded fix for known 'CIViC-to-GraphKB' correspondances
     let name = SUBS[rawName] || rawName;
+
+    const entrezName = rawEntrezName.toLowerCase().trim();
     const joiner = ' and ';
     name = name.replace(' + ', joiner);
     name = name.replace('; ', joiner).toLowerCase().trim();
@@ -76,7 +89,7 @@ const normalizeVariantRecord = ({
     if (name.includes(joiner)) {
         const result = [];
         name.split(joiner).forEach((n) => {
-            result.push(...normalizeVariantRecord({ entrezId, entrezName, name: n.trim() }));
+            result.push(...normalizeGeneVariant({ entrezId, entrezName, name: n.trim() }));
         });
         return result;
     }
@@ -156,8 +169,8 @@ const normalizeVariantRecord = ({
                 rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
             } else {
                 return [
-                    ...normalizeVariantRecord({ entrezId, entrezName, name: `${gene1}-${gene2}` }),
-                    ...normalizeVariantRecord({ entrezId, entrezName, name: tail }),
+                    ...normalizeGeneVariant({ entrezId, entrezName, name: `${gene1}-${gene2}` }),
+                    ...normalizeGeneVariant({ entrezId, entrezName, name: tail }),
                 ];
             }
         }
@@ -213,8 +226,8 @@ const normalizeVariantRecord = ({
     } if (match = /^(\w+\s+fusion)\s+([a-z]\d+\S+)$/i.exec(name)) {
         const [, fusion, resistanceMutation] = match;
         const result = [];
-        result.push(...normalizeVariantRecord({ entrezId, entrezName, name: fusion }));
-        result.push(...normalizeVariantRecord({ entrezId, entrezName, name: resistanceMutation }));
+        result.push(...normalizeGeneVariant({ entrezId, entrezName, name: fusion }));
+        result.push(...normalizeGeneVariant({ entrezId, entrezName, name: resistanceMutation }));
         return result;
     } if (match = /^(.*)\s+mutations?$/.exec(name)) {
         const [, gene] = match;
@@ -241,173 +254,373 @@ const normalizeVariantRecord = ({
     return [{ reference1: { ...referenceGene }, type: name }];
 };
 
+
 /**
- * Given some normalized variant record from CIViC,
- * load into graphkb, create links and return the record
+ * Normalize CIViC Factors variant record as GraphKB Signatures/signature's CVs
  *
- * @param {ApiConnection} conn the connection to GraphKB
- * @param {Object} normalizedVariant the normalized variant record
- * @param {Object} feature the gene feature already grabbed from GraphKB
+ * @param {object} record the raw variant record from CIViC
  * @returns {object[]}
  */
-const uploadNormalizedVariant = async (conn, normalizedVariant, feature) => {
-    let result;
+const normalizeFactorVariant = (record) => {
+    const { feature: { featureInstance } } = record;
 
-    if (!normalizedVariant.positional && /^\s*rs\d+\s*$/gi.exec(normalizedVariant.type)) {
-        const [rsVariant] = await _snp.fetchAndLoadByIds(conn, [normalizedVariant.type]);
+    switch (featureInstance.name) {
+        case 'TMB':
+            return [{
+                reference1: {
+                    class: 'Signature', // flag to escape gene fetching/upload
+                    name: 'high mutation burden',
+                },
+                type: 'high signature',
+            }];
+        // TODO: Add support for other factors
+        case 'Methylation signature':
+        case 'Kataegis':
+        case 'CK':
+        default:
+            throw new NotImplementedError(
+                `unable to process Factor ${featureInstance.name} ${record.name}`,
+            );
+    }
+};
 
-        if (rsVariant) {
-            result = rsVariant;
-        } else {
-            throw new Error(`unable to fetch variant by RSID (${normalizedVariant.type})`);
+
+/**
+ * Normalize CIViC Fusion variant record as GraphKB CVs
+ *
+ * @param {object} record the raw variant record from CIViC
+ * @returns {object[]} array of 1 normalized variant
+ */
+const normalizeFusionVariant = (record) => {
+    const {
+        feature: {
+            featureInstance: {
+                fivePrimeGene,
+                threePrimeGene,
+            },
+        },
+    } = record;
+
+    if (fivePrimeGene && threePrimeGene) {
+        return [{
+            reference1: {
+                name: fivePrimeGene.name.toLowerCase().trim(),
+                sourceId: `${fivePrimeGene.entrezId || ''}`,
+            },
+            reference2: {
+                name: threePrimeGene.name.toLowerCase().trim(),
+                sourceId: `${threePrimeGene.entrezId || ''}`,
+            },
+            type: 'fusion',
+        }];
+    }
+    if (fivePrimeGene) {
+        return [{
+            reference1: {
+                name: fivePrimeGene.name.toLowerCase().trim(),
+                sourceId: `${fivePrimeGene.entrezId || ''}`,
+            },
+            type: 'fusion',
+        }];
+    }
+    if (threePrimeGene) {
+        return [{
+            reference1: {
+                name: threePrimeGene.name.toLowerCase().trim(),
+                sourceId: `${threePrimeGene.entrezId || ''}`,
+            },
+            type: 'fusion',
+        }];
+    }
+    throw new Error('fivePrimeGene and/or threePrimeGene expected on Fusion variant');
+};
+
+
+/**
+ * Given a CIViC variant record, do the normalization based on the feature type.
+ * Can be more than 1 "GraphKB-normalized" variant per CIViC variant.
+ * Returns the normalized variant(s).
+ *
+ * @param {Object} record the raw variant record from CIViC
+ * @returns {object[]} array of normalized variant(s)
+ */
+const normalizeVariant = (record) => {
+    try {
+        const { feature: { featureInstance } } = record;
+        const featureType = featureInstance.__typename;
+
+        switch (featureType) {
+            case 'Gene':
+                // reformatting passed args for legacy purpose
+                return normalizeGeneVariant({
+                    entrezId: featureInstance.entrezId,
+                    entrezName: featureInstance.name,
+                    name: record.name,
+                });
+            case 'Factor':
+                return normalizeFactorVariant(record);
+            case 'Fusion':
+                return normalizeFusionVariant(record);
+            default:
+                throw new NotImplementedError(
+                    `unable to process variant's feature of type ${featureType}`,
+                );
         }
-    } else {
-        let content = {};
+    } catch (err) {
+        logger.error(`unable to normalize the variant (id=${record.id}, name=${record.name})`);
+        throw err;
+    }
+};
 
-    if (normalizedVariant.positional) {
-        content = parseVariant(normalizedVariant.variant, false).toJSON();
+
+/**
+ * Get reference records for the new variant.
+ * Upload if needed (only if gene; signatures needs to be creates using the ontology loader)
+ *
+ * @param {ApiConnection} conn the connection to GraphKB
+ * @param {Object} normalizedVariant the normalized variant record
+ */
+const uploadReferences = async (conn, normalizedVariant) => {
+    const { reference1: r1, reference2: r2 } = normalizedVariant;
+
+    // r2 can be undefined, r1 cannot
+    if (!r1) {
+        // Shouldn't happen; means there is an error in the normalization code
+        throw new Error('reference1 is mandatory on normalizedVariant');
     }
 
-        // try to fetch civic specific term first
+    // Signature (from civic Factor) as reference
+    if (r1.class === 'Signature') {
         try {
-            variantType = await conn.getVocabularyTerm(
-                normalizedVariant.type || content.type,
-                SOURCE_DEFN.name,
-            );
+            return [await conn.getUniqueRecordBy({
+                filters: { name: r1.name },
+                neighbors: 0,
+                target: r1.class,
+            })];
         } catch (err) {
-            try {
-                variantType = await conn.getVocabularyTerm(normalizedVariant.type || content.type);
-            } catch (e) {
-                throw new Error(`Unable to upload CIVIC variant (${normalizedVariant}})`);
-            }
+            throw new Error(`failed to fetch variant's ${r1.class} Reference ${r1.name}`);
         }
-        content.type = rid(variantType);
+    }
 
-        // get the reference elements
-        let reference2,
-            reference1 = feature;
+    // Gene(s) as reference(s)
+    const references = [];
 
-        if (normalizedVariant.reference2) {
-            if (normalizedVariant.reference2.sourceId === feature.sourceId) {
-                reference2 = feature;
-                // fetch reference1
-                [reference1] = await _entrezGene.fetchAndLoadBySymbol(conn, normalizedVariant.reference1.name);
+    for (const ref of [r1, r2]) {
+        if (ref) {
+            let reference;
 
-                if (!reference1) {
-                    throw new Error(`Gene name not found in NCBI's Entrez gene database (${normalizedVariant.reference1.name}})`);
+            try {
+                if (ref.sourceId) {
+                    [reference] = await _entrezGene.fetchAndLoadByIds(conn, [ref.sourceId]);
                 }
-            } else if (normalizedVariant.reference1.sourceId !== feature.sourceId) {
-                throw new ParsingError(`Feature ID input (${feature.sourceId}) does not match the linked gene IDs (${normalizedVariant.reference1.sourceId},${normalizedVariant.reference2.sourceId})`);
-            } else {
-                // fetch reference2
-                [reference2] = await _entrezGene.fetchAndLoadBySymbol(conn, normalizedVariant.reference2.name);
+                if (!ref.sourceId && ref.name) {
+                    [reference] = await _entrezGene.fetchAndLoadBySymbol(conn, ref.name);
+                }
+                if (!ref.sourceId && !ref.name) {
+                    // Shouldn't happen; means there is an error in the normalization code
+                    throw new Error('name property is mandatory on normalizedVariant reference');
+                }
+                references.push(reference);
+            } catch (err) {
+                logger.error(`failed to fetch variant's feature: ${ref.name}`);
+                throw err;
             }
         }
+    }
+    return references;
+};
 
-        content.reference1 = rid(reference1);
 
-        if (reference2) {
-            content.reference2 = rid(reference2);
-        }
-        result = await conn.addVariant({
-            content,
-            existsOk: true,
-            target: normalizedVariant.positional
-                ? 'PositionalVariant'
-                : 'CategoryVariant',
-        });
-    }
+/**
+ * Get or create inferred/inferring variant(s) and create linking Infers edge(s)
+ *
+ * @param {ApiConnection} conn the connection to GraphKB
+ * @param {Object} normalizedVariant the normalized variant record
+ * @param {Object} result the GraphKB variant record to connect edges from/to
+ * @returns {object[]}
+ */
+const uploadInferences = async (conn, normalizedVariant, result) => {
+    const links = { inferredBy: [], infers: [] };
+    const variants = { inferred: [], inferring: [] };
 
-    // now create any links
+    // Outgoing, if any
     for (const variant of normalizedVariant.infers || []) {
-        const infers = await uploadNormalizedVariant(conn, variant, feature);
-        await conn.addRecord({
-            content: { in: rid(infers), out: rid(result) },
-            existsOk: true,
-            fetchExisting: false,
-            target: 'Infers',
-        });
+        try {
+            // Creates or get the variant on the incomming side
+            const infers = await uploadVariant(conn, variant);
+            variants.inferred.push(infers);
+
+            // Creates the edge
+            links.infers.push(
+                await conn.addRecord({
+                    content: { in: rid(infers), out: rid(result) },
+                    existsOk: true,
+                    fetchExisting: false,
+                    target: 'Infers',
+                }),
+            );
+        } catch (err) {
+            // Non-blocking error
+            logger.warn(`Error while uploading inferred variant; ${JSON.stringify(variant)}`);
+        }
     }
 
+    // Incomming, if any
     for (const variant of normalizedVariant.inferredBy || []) {
-        const inferredBy = await uploadNormalizedVariant(conn, variant, feature);
-        await conn.addRecord({
-            content: { in: rid(result), out: rid(inferredBy) },
-            existsOk: true,
-            fetchExisting: false,
-            target: 'Infers',
-        });
+        try {
+            // Creates or get the variant on the outgoing side
+            const inferredBy = await uploadVariant(conn, variant);
+            variants.inferring.push(inferredBy);
+
+            // Creates the edge
+            links.inferredBy.push(
+                await conn.addRecord({
+                    content: { in: rid(result), out: rid(inferredBy) },
+                    existsOk: true,
+                    fetchExisting: false,
+                    target: 'Infers',
+                }),
+            );
+        } catch (err) {
+            // Non-blocking error
+            logger.warn(`Error while uploading inferring variant; ${JSON.stringify(variant)}`);
+        }
     }
 
-    return result;
+    // Return for testing purpose only
+    return { links, variants };
 };
 
+
 /**
- * Given some variant record and a feature, process the variant and return a GraphKB equivalent
+ * Given a normalized CIViC variant record, upload to GraphKB,
+ * create any given links and return the GraphKB variant record.
  *
  * @param {ApiConnection} conn the connection to GraphKB
- * @param {Object} civicVariantRecord the raw variant record from CIViC
- * @param {Object} feature the gene feature already grabbed from GraphKB
+ * @param {Object} normalizedVariant the normalized variant record
  * @returns {object[]}
  */
-const processVariantRecord = async (conn, civicVariantRecord, feature) => {
-    const { feature: { featureInstance } } = civicVariantRecord;
-    let entrezId,
-        entrezName;
-
-    // featureInstance
-    if (featureInstance.__typename === 'Gene') {
-        entrezId = featureInstance.entrezId;
-        entrezName = featureInstance.name;
-    } else if (featureInstance.__typename === 'Factor') {
-        // TODO: Deal with __typename === 'Factor'
-        // No actual case as April 22nd, 2024
-        throw new NotImplementedError(
-            'unable to process variant\'s feature of type Factor',
+const uploadVariant = async (conn, normalizedVariant) => {
+    let uploadedVariant;
+
+    // RSID Variant exception handled first
+    if (!normalizedVariant.positional && /^\s*rs\d+\s*$/gi.exec(normalizedVariant.type)) {
+        // Create Variant VERTEX in GraphKB
+        [uploadedVariant] = await _snp.fetchAndLoadByIds(conn, [normalizedVariant.type]);
+
+        if (uploadedVariant) {
+            // Create Inferring/inferred variant and Infers edge in GraphKB
+            if (normalizedVariant.infers || normalizedVariant.inferredBy) {
+                await uploadInferences(conn, normalizedVariant, uploadedVariant);
+            }
+        } else {
+            throw new Error(`unable to fetch variant by RSID (${normalizedVariant.type})`);
+        }
+        return uploadedVariant;
+    }
+
+    // Variant content
+    let content = {};
+
+    if (normalizedVariant.positional) {
+        content = parseVariant(normalizedVariant.variant, false).toJSON();
+    }
+
+    // Variant type
+    let variantType;
+
+    try {
+        // try to fetch civic specific term first
+        variantType = await conn.getVocabularyTerm(
+            normalizedVariant.type || content.type,
+            SOURCE_DEFN.name,
         );
+    } catch (err) {
+        // try to fetch term from any source
+        variantType = await conn.getVocabularyTerm(normalizedVariant.type || content.type);
     }
+    content.type = rid(variantType);
 
-    // Raw variant from CIViC to normalize & upload to GraphKB if needed
-    const rawVariant = {
-        entrezId,
-        entrezName,
-        name: civicVariantRecord.name,
-    };
+    // Variant references
+    const [reference1, reference2] = await uploadReferences(conn, normalizedVariant);
+    content.reference1 = rid(reference1);
 
-    // Trying cache first
-    const fromCache = VARIANT_CACHE.get(JSON.stringify(rawVariant));
+    if (reference2) {
+        content.reference2 = rid(reference2);
+    }
 
-    if (fromCache) {
-        if (fromCache.err) {
-            throw new Error('Variant record previously processed with errors');
-        }
-        if (fromCache.result) {
-            return fromCache.result;
-        }
+    // Create Variant VERTEX in GraphKB
+    uploadedVariant = await conn.addVariant({
+        content,
+        existsOk: true,
+        target: normalizedVariant.positional
+            ? 'PositionalVariant'
+            : 'CategoryVariant',
+    });
+
+    // Create Inferring/inferred variant and Infers edge in GraphKB
+    if (normalizedVariant.infers || normalizedVariant.inferredBy) {
+        await uploadInferences(conn, normalizedVariant, uploadedVariant);
     }
 
-    const result = [];
+    return uploadedVariant;
+};
+
 
-    try {
-        // Normalizing
-        const variants = normalizeVariantRecord(rawVariant);
+/**
+ * Upload an array of normalized CIViC variants to GraphKB.
+ * Returns an array of corresponding GraphKB Variant record(s).
+ *
+ * @param {ApiConnection} conn the connection to GraphKB
+ * @param {Object[]} normalizedVariants an array of normalized CIViC variant records
+ * @returns {object[]}
+ */
+const uploadVariants = async (conn, normalizedVariants) => {
+    const uploadedVariants = [];
+
+    for (const normalizedVariant of normalizedVariants) {
+        // console.log(JSON.stringify(normalizedVariant));
+
+        // Trying cache first
+        const key = JSON.stringify(normalizedVariant);
+        const fromCache = VARIANT_CACHE.get(key);
+
+        if (fromCache) {
+            if (fromCache.err) {
+                throw new Error('Variant record previously processed with errors');
+            }
+            if (fromCache.uploaded) {
+                uploadedVariants.push(fromCache.uploaded);
+                continue;
+            }
+        }
 
         // Uploading
-        for (const normalizedVariant of variants) {
-            result.push(await uploadNormalizedVariant(conn, normalizedVariant, feature));
+        try {
+            const uploaded = await uploadVariant(conn, normalizedVariant);
+            uploadedVariants.push(uploaded);
+            VARIANT_CACHE.set(key, { uploaded });
+        } catch (err) {
+            VARIANT_CACHE.set(key, { err });
+            logger.error(`failed to upload variant ${JSON.stringify(normalizedVariant)}`);
+            throw err;
         }
-    } catch (err) {
-        VARIANT_CACHE.set(JSON.stringify(rawVariant), { err });
-        throw err;
     }
 
-    VARIANT_CACHE.set(JSON.stringify(rawVariant), { result });
-    return result;
+    // console.log({uploadedVariants: uploadedVariants[0]['@rid']});
+    return uploadedVariants;
 };
 
+
 module.exports = {
+    NotImplementedError,
     compareGeneNames,
-    normalizeVariantRecord,
-    processVariantRecord,
-    uploadNormalizedVariant,
+    normalizeFactorVariant,
+    normalizeFusionVariant,
+    normalizeGeneVariant,
+    normalizeVariant,
+    uploadInferences,
+    uploadReferences,
+    uploadVariant,
+    uploadVariants,
 };

From de8551412daef971404bac84a4491e83eed07289 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:09:22 -0800
Subject: [PATCH 13/29] Linting civic index.js

---
 src/civic/index.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 262e1d2a..aa0f3228 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -56,10 +56,10 @@ const incrementCounts = (initial, updates) => {
  *
  * @param {object} param0
  * @param {ApiConnection} param0.conn the api connection object for GraphKB
- * @param {?boolean} param0.deleteDeprecated deletion of existing GraphKB Statements related to deprecated evidence(s)
+ * @param {?boolean} param0.deleteDeprecated delete GraphKB Statements if deprecated evidence(s)
  * @param {string} param0.errorLogPrefix prefix to the generated error json file
  * @param {number} param0.maxRecords limit of EvidenceItem records to be processed and upload
- * @param {?boolean} param0.noDeleteOnUnmatched no deletion of existing GraphKB Statements related to unmatched combination(s)
+ * @param {?boolean} param0.noDeleteOnUnmatched don't delete GraphKB St. if unmatched combination(s)
  * @param {?boolean} param0.noUpdate no update of existing GraphKB Statements
  * @param {string[]} param0.trustedCurators a list of curator IDs for submitted-only EvidenceItems
  * @param {?string} param0.url url to use as the base for accessing the civic ApiConnection

From e23f2d022773970de5dcb675c7f2076ab1cc33b9 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 16 Dec 2024 11:09:43 -0800
Subject: [PATCH 14/29] Add tests for civic variants

---
 test/civic/civic.variant.test.js | 395 ++++++++++++++++++++++++++-----
 1 file changed, 342 insertions(+), 53 deletions(-)

diff --git a/test/civic/civic.variant.test.js b/test/civic/civic.variant.test.js
index 4814157c..833a9c23 100644
--- a/test/civic/civic.variant.test.js
+++ b/test/civic/civic.variant.test.js
@@ -1,9 +1,129 @@
 /* eslint-disable jest/no-disabled-tests */
-const { normalizeVariantRecord } = require('../../src/civic/variant');
+const {
+    normalizeFactorVariant,
+    normalizeFusionVariant,
+    normalizeGeneVariant,
+    normalizeVariant,
+    NotImplementedError,
+    uploadInferences,
+    uploadReferences,
+    uploadVariant,
+    uploadVariants,
+} = require('../../src/civic/variant');
+
+
+/*
+    SYNCHRONOUS TESTS
+*/
+
+const civicVariantRecordsFactor = [
+    {
+        feature: { featureInstance: { __typename: 'Factor', name: 'TMB' } },
+        id: 123,
+        name: 'abc',
+    },
+];
+const civicVariantRecordsFusion = [
+    {
+        feature: {
+            featureInstance: {
+                __typename: 'Fusion',
+                fivePrimeGene: {
+                    entrezId: 673,
+                    id: 5,
+                    name: 'BRAF',
+                },
+            },
+        },
+        id: 123,
+    },
+    {
+        feature: {
+            featureInstance: {
+                __typename: 'Fusion',
+                threePrimeGene: {
+                    entrezId: 238,
+                    id: 1,
+                    name: 'ALK',
+                },
+            },
+        },
+        id: 123,
+    },
+    {
+        feature: {
+            featureInstance: {
+                __typename: 'Fusion',
+                fivePrimeGene: {
+                    entrezId: 673,
+                    id: 5,
+                    name: 'BRAF',
+                },
+                threePrimeGene: {
+                    entrezId: 238,
+                    id: 1,
+                    name: 'ALK',
+                },
+            },
+        },
+        id: 123,
+    },
+];
+const civicVariantRecordsGene = [
+    {
+        feature: { featureInstance: { __typename: 'Gene', entrezId: 672, name: 'BRCA1' } },
+        name: 'Mutation',
+    },
+];
+
+
+describe('normalizeFactorVariant', () => {
+    test('testnormalizeFactorVariant', () => {
+        const normalizedVariants = normalizeFactorVariant(civicVariantRecordsFactor[0]);
+        expect(normalizedVariants.length).toEqual(1);
+        expect(normalizedVariants[0]).toEqual({
+            reference1: {
+                class: 'Signature',
+                name: 'high mutation burden',
+            },
+            type: 'high signature',
+        });
+    });
+});
+
+describe('normalizeFusionVariant', () => {
+    test('testnormalizeFusionVariantFivePrimeGeneOnly', () => {
+        const normalizedVariants = normalizeFusionVariant(civicVariantRecordsFusion[0]);
+        expect(normalizedVariants.length).toEqual(1);
+        expect(normalizedVariants[0]).toEqual({
+            reference1: { name: 'braf', sourceId: '673' },
+            type: 'fusion',
+        });
+    });
+
+    test('testnormalizeFusionVariantThreePrimeGeneOnly', () => {
+        const normalizedVariants = normalizeFusionVariant(civicVariantRecordsFusion[1]);
+        expect(normalizedVariants.length).toEqual(1);
+        expect(normalizedVariants[0]).toEqual({
+            reference1: { name: 'alk', sourceId: '238' },
+            type: 'fusion',
+        });
+    });
 
-describe('normalizeVariantRecord', () => {
+    test('testnormalizeFusionVariantBothGenes', () => {
+        const normalizedVariants = normalizeFusionVariant(civicVariantRecordsFusion[2]);
+        expect(normalizedVariants.length).toEqual(1);
+        expect(normalizedVariants[0]).toEqual({
+            reference1: { name: 'braf', sourceId: '673' },
+            reference2: { name: 'alk', sourceId: '238' },
+            type: 'fusion',
+        });
+    });
+});
+
+describe('normalizeGeneVariant', () => {
     test('exon mutation', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'gene',
             name: 'EXON 12 MUTATION',
@@ -19,7 +139,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('deleterious mutation', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'gene',
             name: 'DELETRIOUS MUTATION',
@@ -31,7 +151,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('phosphorylation variant', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'gene',
             name: 'Y1234 phosphorylation',
@@ -44,7 +164,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('single gene fusion with missense mutation', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'ALK FUSION G1202R',
@@ -63,7 +183,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('multi-gene fusion with 2 resistance mutations (dash notation)', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'alk',
             name: 'EML4-ALK G1202R-L1198F',
@@ -88,7 +208,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('multi-gene fusion', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NRG1',
             name: 'CD74-NRG1',
@@ -103,7 +223,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('fusion with multiple variants', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'LMNA-NTRK1 G595R AND G667C',
@@ -128,7 +248,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('fusion with multiple variants (colon sep)', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'LMNA::NTRK1 G595R AND G667C',
@@ -154,7 +274,7 @@ describe('normalizeVariantRecord', () => {
 
     test('corrects deprecated indel syntax', () => {
         // S111C (c.330CA>TT)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'S111C (c.330CA>TT)',
@@ -173,17 +293,8 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
-    test.skip('multiple variants with plus notation', () => {
-        // V600E+V600M
-        // E2014K + E2419K
-    });
-
-    test.skip('missense and amplification', () => {
-        // V600E AMPLIFICATION
-    });
-
     test('categorical variant', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'UNDEREXPRESSION',
@@ -198,7 +309,7 @@ describe('normalizeVariantRecord', () => {
 
     test('protein truncation with cds notation', () => {
         // e46* (c.136g>t)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'E46* (c.136G>T)',
@@ -220,7 +331,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('categorical variant with spaces', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'DNA BINDING DOMAIN MUTATION',
@@ -235,7 +346,7 @@ describe('normalizeVariantRecord', () => {
 
     test('regular missense mutation', () => {
         // R132H
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NTRK1',
             name: 'R132H',
@@ -251,7 +362,7 @@ describe('normalizeVariantRecord', () => {
 
     test('plural for single gene fusion', () => {
         // ALK FUSIONS
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'NRG1',
             name: 'NRG1 fusions',
@@ -267,7 +378,7 @@ describe('normalizeVariantRecord', () => {
     test('fusion with exon positions', () => {
         // EML4-ALK E20;A20
         // ALK FUSIONS
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'EML4-ALK E20;A20',
@@ -285,7 +396,7 @@ describe('normalizeVariantRecord', () => {
     test('fusion with new exon notation', () => {
         // EWSR1-FLI1 e7-e6
         // FLI1 Fusion
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'FLI1',
             name: 'EWSR1-FLI1 e7-e6',
@@ -303,7 +414,7 @@ describe('normalizeVariantRecord', () => {
     test('fusion with reference2 input gene', () => {
         // EML4-ALK E20;A20
         // ALK FUSIONS
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'EML4',
             name: 'EML4-ALK E20;A20',
@@ -320,7 +431,7 @@ describe('normalizeVariantRecord', () => {
 
     test('abl fusion', () => {
         // BCR-ABL
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'BCR-ABL',
@@ -336,7 +447,7 @@ describe('normalizeVariantRecord', () => {
 
     test('cds notation', () => {
         // BCR-ABL
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'c.123G>T',
@@ -352,7 +463,7 @@ describe('normalizeVariantRecord', () => {
 
     test('exon range deletion', () => {
         // BCR-ABL
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'exon 2-3 deletion',
@@ -367,7 +478,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('frameshift with cds', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 't133lfs*26 (c.397dela)',
@@ -389,7 +500,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('protein indel with cds', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 't133lfs*26 (c.397dela)',
@@ -412,7 +523,7 @@ describe('normalizeVariantRecord', () => {
 
     test('simple gene mutation', () => {
         // BCR-ABL
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'ABL1 mutations',
@@ -426,7 +537,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('exon plural mutations', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'exon 3 mutations',
@@ -441,7 +552,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('mutations', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ABL1',
             name: 'mutations',
@@ -454,13 +565,9 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
-    test.skip('germline notation', () => {
-        // DPYD*2A HOMOZYGOSITY
-    });
-
     test('splice site mutation', () => {
         // F547 SPLICE SITE MUTATION
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'F547 SPLICE SITE MUTATION',
@@ -477,7 +584,7 @@ describe('normalizeVariantRecord', () => {
     test('protein deletion with cds deletion sequence', () => {
         // r79_s80del (c.236_241delgcagtc)
         // r82_v84del (c.244_252del)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'r79_s80del (c.236_241delgcagtc)',
@@ -499,7 +606,7 @@ describe('normalizeVariantRecord', () => {
     });
 
     test('protein deletion with cds deletion no sequence', () => {
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'r82_v84del (c.244_252del)',
@@ -522,7 +629,7 @@ describe('normalizeVariantRecord', () => {
 
     test('protein dup with cds dup', () => {
         // p.s193_c196dupstsc (c.577_588dupagcaccagctgc)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'p.s193_c196dupstsc (c.577_588dupagcaccagctgc)',
@@ -545,7 +652,7 @@ describe('normalizeVariantRecord', () => {
 
     test('protein with cds notation', () => {
         // A122I (c.364_365GC>AT)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'A122I (c.364_365GC>AT)',
@@ -568,7 +675,7 @@ describe('normalizeVariantRecord', () => {
 
     test('OR-able position no alt seq', () => {
         // G12/G13
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'G12/G13',
@@ -582,13 +689,9 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
-    test.skip('catalogue variant', () => {
-        // RS3910384
-    });
-
     test('semi-colon delimited variants', () => {
         // A50A (c.150C>G); Splicing alteration (c.463-1G>T)
-        const variants = normalizeVariantRecord({
+        const variants = normalizeGeneVariant({
             entrezId: 1,
             entrezName: 'ALK',
             name: 'A50A (c.150C>G); Splicing alteration (c.463-1G>T)',
@@ -618,6 +721,23 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
+    test.skip('multiple variants with plus notation', () => {
+        // V600E+V600M
+        // E2014K + E2419K
+    });
+
+    test.skip('missense and amplification', () => {
+        // V600E AMPLIFICATION
+    });
+
+    test.skip('germline notation', () => {
+        // DPYD*2A HOMOZYGOSITY
+    });
+
+    test.skip('catalogue variant', () => {
+        // RS3910384
+    });
+
     test.skip('duplicate fusion', () => {
         // AGGF1-PDGFRB, AGGF1-PDGFRB C843G
     });
@@ -628,7 +748,7 @@ describe('normalizeVariantRecord', () => {
 
     describe('bad notation should return as vocabulary', () => {
         test('ERBB2 G776INSV_G/C', () => {
-            const variants = normalizeVariantRecord({
+            const variants = normalizeGeneVariant({
                 entrezId: 1,
                 entrezName: 'ERBB2',
                 name: 'ERBB2 G776INSV_G/C',
@@ -640,7 +760,7 @@ describe('normalizeVariantRecord', () => {
         });
 
         test('exon1 151nt del; Null (Partial deletion of Exon 1)', () => {
-            const variants = normalizeVariantRecord({
+            const variants = normalizeGeneVariant({
                 entrezId: 1,
                 entrezName: 'ERBB2',
                 name: 'exon1 151nt del; Null (Partial deletion of Exon 1)',
@@ -655,3 +775,172 @@ describe('normalizeVariantRecord', () => {
         });
     });
 });
+
+describe('normalizeVariant', () => {
+    [
+        civicVariantRecordsFactor[0],
+        civicVariantRecordsFusion[0],
+        civicVariantRecordsGene[0],
+
+    ].forEach((record) => {
+        test(`testNormalizeVariantFeatureType${record.feature.featureInstance.__typename}`, () => {
+            expect(normalizeVariant(record).length).toBe(1);
+        });
+    });
+
+    test('testNormalizeVariantFeatureTypeNotImplemented', () => {
+        expect(() => {
+            normalizeVariant(
+                { feature: { featureInstance: { __typename: 'Other' } } },
+            );
+        }).toThrow(NotImplementedError);
+    });
+});
+
+
+/*
+    ASYNCHRONOUS TESTS
+*/
+
+const mockConn = () => ({
+    addRecord: jest.fn().mockResolvedValue({ '@rid': '#', reference1: '#' }), // used by Entrez loader
+    addSource: jest.fn().mockResolvedValue({ '@rid': '#', reference1: '#' }), // used by Entrez loader
+    addVariant: jest.fn().mockResolvedValue({ '@rid': '#123:45' }),
+    getUniqueRecordBy: jest.fn().mockResolvedValue({ '@rid': '#678:90', reference1: '#' }),
+    getVocabularyTerm: jest.fn().mockResolvedValue({ '@rid': '#' }),
+});
+const conn = mockConn();
+
+
+describe.skip('uploadReferences', () => {
+    const normalizedVariants = [
+        { },
+        { reference1: { } },
+        { reference1: { class: 'Signature', name: '' } },
+        { reference1: { sourceId: '123' } },
+        { reference1: { name: 'abc' } },
+        { reference1: { sourceId: '123' }, reference2: { sourceId: '456' } },
+    ];
+
+    test('testUploadReferencesNoReference1', async () => {
+        await expect(
+            uploadReferences(conn, normalizedVariants[0]),
+        ).rejects.toThrow('reference1 is mandatory on normalizedVariant');
+    });
+
+    test('testUploadReferencesNoName', async () => {
+        await expect(
+            uploadReferences(conn, normalizedVariants[1]),
+        ).rejects.toThrow('name property is mandatory on normalizedVariant reference');
+    });
+
+    test('testUploadReferencesSignature', async () => {
+        const [reference1, reference2] = await uploadReferences(conn, normalizedVariants[2]);
+        expect(reference1).toEqual({ '@rid': '#678:90', reference1: '#' });
+        expect(reference2).toEqual(undefined);
+    });
+
+    test('testUploadReferencesWithSourceId', async () => {
+        const [reference1, reference2] = await uploadReferences(conn, normalizedVariants[3]);
+        expect(reference1).toEqual({ '@rid': '#678:90', reference1: '#' });
+        expect(reference2).toEqual(undefined);
+    });
+
+    test('testUploadReferencesWithName', async () => {
+        const [reference1, reference2] = await uploadReferences(conn, normalizedVariants[4]);
+        expect(reference1).toEqual({ '@rid': '#678:90', reference1: '#' });
+        expect(reference2).toEqual(undefined);
+    });
+
+    test('testUploadReferencesWithReference2', async () => {
+        const [reference1, reference2] = await uploadReferences(conn, normalizedVariants[5]);
+        expect(reference1).toEqual({ '@rid': '#678:90', reference1: '#' });
+        expect(reference2).toEqual({ '@rid': '#678:90', reference1: '#' });
+    });
+});
+
+describe.skip('uploadInferences', () => {
+    const normalizedVariants = [
+        {
+            infers: [
+                { reference1: { name: '...' }, type: '...' },
+                { reference1: { name: '...' }, type: '...' },
+            ],
+        },
+        {
+            inferredBy: [
+                { reference1: { name: '...' }, type: '...' },
+                { reference1: { name: '...' }, type: '...' },
+                { reference1: { name: '...' }, type: '...' },
+            ],
+        },
+    ];
+
+    test('testUploadInferencesInfers', async () => {
+        const { links, variants } = await uploadInferences(conn, normalizedVariants[0], { '@rid': '#' });
+        expect(links.infers.length).toEqual(2);
+        expect(variants.inferred.length).toEqual(2);
+    });
+
+    test('testUploadInferencesInferredBy', async () => {
+        const { links, variants } = await uploadInferences(conn, normalizedVariants[1], { '@rid': '#' });
+        expect(links.inferredBy.length).toEqual(3);
+        expect(variants.inferring.length).toEqual(3);
+    });
+});
+
+describe.skip('uploadVariant', () => {
+    const normalizedVariants = [
+        { type: 'rs123' },
+        { positional: true, reference1: { name: 'egfr', sourceId: 1956 }, variant: 'c.1del' },
+        { reference1: { name: 'egfr', sourceId: 1956 }, type: 'mutation' },
+    ];
+
+    test('testUploadVariantRSID', async () => {
+        const result = await uploadVariant(conn, normalizedVariants[0]);
+        expect(result).toEqual({ '@rid': '#678:90', reference1: '#' });
+    });
+
+    test('testUploadVariantPositional', async () => {
+        const result = await uploadVariant(conn, normalizedVariants[1]);
+        expect(result).toEqual({ '@rid': '#123:45' });
+    });
+
+    test('testUploadVariantCategory', async () => {
+        const result = await uploadVariant(conn, normalizedVariants[2]);
+        expect(result).toEqual({ '@rid': '#123:45' });
+    });
+});
+
+describe('uploadVariants', () => {
+    const normalizedVariants = [
+        // Factor
+        {
+            reference1: {
+                class: 'Signature',
+                name: 'high mutation burden',
+            },
+            type: 'high signature',
+        },
+        // Fusion
+        {
+            reference1: { name: 'braf', sourceId: '673' },
+            reference2: { name: 'alk', sourceId: '238' },
+            type: 'fusion',
+        },
+        // Gene
+        {
+            reference1: { name: 'braf', sourceId: '673' },
+            type: 'mutation',
+        },
+    ];
+
+    test('testuploadVariants', async () => {
+        const uploadedVariants = await uploadVariants(conn, normalizedVariants);
+        expect(uploadedVariants.length).toEqual(3);
+
+        for (let i = 0; i < uploadedVariants.length; i++) {
+            expect(uploadedVariants[i]).toEqual({ '@rid': '#123:45' });
+        }
+    });
+});

From b70cc9a6966ac8df301712289da0a3244b9f1bee Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 12:57:29 -0800
Subject: [PATCH 15/29] Revert parseVariantDecorator and use jsonifyVariant
 instead

---
 src/PMC4232638/index.js              |  8 ++---
 src/cancergenomeinterpreter/index.js | 13 ++++----
 src/cancerhotspots/index.js          | 13 ++++----
 src/cgl/index.js                     |  8 ++---
 src/civic/variant.js                 | 14 +++++----
 src/cosmic/resistance.js             | 11 +++----
 src/docm/index.js                    |  9 ++----
 src/entrez/snp.js                    | 10 ++-----
 src/moa/index.js                     | 13 ++++----
 src/oncokb/index.js                  | 11 +++----
 src/util.js                          | 44 ----------------------------
 src/variants/index.js                |  8 ++---
 12 files changed, 45 insertions(+), 117 deletions(-)

diff --git a/src/PMC4232638/index.js b/src/PMC4232638/index.js
index 5334b3b8..979d7846 100644
--- a/src/PMC4232638/index.js
+++ b/src/PMC4232638/index.js
@@ -1,16 +1,12 @@
 const readXlsxFile = require('read-excel-file/node');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 const { logger } = require('../logging');
 const { rid } = require('../graphkb');
 const _pubmed = require('../entrez/pubmed');
 const _entrezGene = require('../entrez/gene');
 const { PMC4232638: SOURCE_DEFN } = require('../sources');
 
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
-
 const TP53_COLS = {
     DOM: 'Functional categories for TP53 - Dominant negative activity',
     GOF: 'Functional categories for TP53 - Gain of function',
@@ -137,7 +133,7 @@ const uploadFile = async ({ conn, filename }) => {
         logger.info(`loading: ${row.Gene}:${row['Amino acid change']}`);
 
         try {
-            const parsed = parseVariant(`p.${row['Amino acid change']}`, false).toJSON();
+            const parsed = jsonifyVariant(parseVariant(`p.${row['Amino acid change']}`, false));
             const [gene] = await _entrezGene.fetchAndLoadBySymbol(conn, row.Gene);
             const relevance = await conn.getVocabularyTerm(row.relevance);
             const evidence = await _pubmed.fetchAndLoadByIds(conn, row.evidence);
diff --git a/src/cancergenomeinterpreter/index.js b/src/cancergenomeinterpreter/index.js
index d07638fa..42ebf0ed 100644
--- a/src/cancergenomeinterpreter/index.js
+++ b/src/cancergenomeinterpreter/index.js
@@ -1,9 +1,6 @@
 const fs = require('fs');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     loadDelimToJson,
@@ -220,7 +217,7 @@ const processVariants = async ({ conn, row, source }) => {
     }
 
     if (genomic && !isCat) {
-        const parsed = parseVariant(genomic).toJSON();
+        const parsed = jsonifyVariant(parseVariant(genomic));
         const reference1 = await conn.getUniqueRecordBy({
             filters: {
                 AND: [
@@ -245,7 +242,7 @@ const processVariants = async ({ conn, row, source }) => {
     }
 
     if (protein && !isCat) {
-        const parsed = parseVariant(`${gene}:${protein.split(':')[1]}`).toJSON();
+        const parsed = jsonifyVariant(parseVariant(`${gene}:${protein.split(':')[1]}`));
         const type = await conn.getVocabularyTerm(parsed.type);
         proteinVariant = await conn.addVariant({
             content: { ...parsed, reference1: rid(gene1Record), type },
@@ -254,7 +251,7 @@ const processVariants = async ({ conn, row, source }) => {
         });
     }
     if (transcript && cds && !isCat) {
-        const parsed = parseVariant(`${transcript}:${cds}`).toJSON();
+        const parsed = jsonifyVariant(parseVariant(`${transcript}:${cds}`));
         const reference1 = await conn.getUniqueRecordBy({
             filters: { AND: [{ biotype: 'transcript' }, { sourceId: transcript }, { sourceIdVersion: null }] },
             sort: orderPreferredOntologyTerms,
@@ -268,7 +265,7 @@ const processVariants = async ({ conn, row, source }) => {
         });
     }
     if (exonic && !isCat) {
-        const parsed = parseVariant(`${gene}:${exonic}`).toJSON();
+        const parsed = jsonifyVariant(parseVariant(`${gene}:${exonic}`));
         const type = await conn.getVocabularyTerm(parsed.type);
         exonicVariant = await conn.addVariant({
             content: { ...parsed, reference1: rid(gene1Record), type },
diff --git a/src/cancerhotspots/index.js b/src/cancerhotspots/index.js
index e048be4b..54c8b9ba 100644
--- a/src/cancerhotspots/index.js
+++ b/src/cancerhotspots/index.js
@@ -5,10 +5,7 @@ const fs = require('fs');
 
 const csv = require('fast-csv');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     convertRowFields,
@@ -104,7 +101,7 @@ const processVariants = async ({ conn, record, source }) => {
             // deletion
             notation = `${notation}${start}_${stop}del${refSeq}`;
         }
-        const variant = parseVariant(notation).toJSON();
+        const variant = jsonifyVariant(parseVariant(notation));
 
         variant.reference1 = rid(reference1);
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
@@ -128,10 +125,10 @@ const processVariants = async ({ conn, record, source }) => {
             [reference1] = await _entrezGene.fetchAndLoadByIds(conn, [geneId]);
             featureCache[geneId] = reference1;
         }
-        const variant = parseVariant(
+        const variant = jsonifyVariant(parseVariant(
             protein.replace(/fs\*\?$/, 'fs'), // ignore uncertain truncations
             false,
-        ).toJSON();
+        ));
         variant.reference1 = rid(reference1);
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
         proteinVariant = rid(await conn.addVariant({
@@ -166,7 +163,7 @@ const processVariants = async ({ conn, record, source }) => {
             featureCache[transcriptId] = reference1;
         }
         // parse the cds variant
-        const variant = parseVariant(cds, false).toJSON();
+        const variant = jsonifyVariant(parseVariant(cds, false));
 
         variant.reference1 = reference1;
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
diff --git a/src/cgl/index.js b/src/cgl/index.js
index 56cca0d5..7881af6f 100644
--- a/src/cgl/index.js
+++ b/src/cgl/index.js
@@ -1,6 +1,6 @@
 const fs = require('fs');
 
-const { parseVariant } = require('@bcgsc-pori/graphkb-parser');
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     loadDelimToJson,
@@ -50,7 +50,7 @@ const loadCdsVariant = async (graphkbConn, transcriptId, cdsNotation) => {
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const cds = rid(await graphkbConn.addVariant({
-        content: { ...variant },
+        content: { ...jsonifyVariant(variant) },
         existsOk: true,
         target: 'PositionalVariant',
     }));
@@ -91,7 +91,7 @@ const loadProteinVariant = async (graphkbConn, gene, proteinNotation) => {
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const protein = rid(await graphkbConn.addVariant({
-        content: { ...variant },
+        content: { ...jsonifyVariant(variant) },
         existsOk: true,
         target: 'PositionalVariant',
     }));
@@ -167,7 +167,7 @@ const loadGenomicVariant = async (graphkbConn, chromosome, position, ref, alt) =
     variant.reference1 = reference1;
     variant.type = rid(await graphkbConn.getVocabularyTerm(variant.type));
     const genomic = rid(await graphkbConn.addVariant({
-        content: { ...variant, assembly: 'hg19' },
+        content: { ...jsonifyVariant(variant), assembly: 'hg19' },
         existsOk: true,
         target: 'PositionalVariant',
     }));
diff --git a/src/civic/variant.js b/src/civic/variant.js
index 346a3a23..684197e2 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -1,14 +1,16 @@
-const { ErrorMixin, ParsingError, parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const {
+    ErrorMixin,
+    jsonifyVariant,
+    parseVariant,
+    ParsingError,
+} = require('@bcgsc-pori/graphkb-parser');
+
 const { rid } = require('../graphkb');
 const _entrezGene = require('../entrez/gene');
 const _snp = require('../entrez/snp');
 const { civic: SOURCE_DEFN } = require('../sources');
 const { logger } = require('../logging');
 
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
-
 class NotImplementedError extends ErrorMixin { }
 
 const VARIANT_CACHE = new Map();
@@ -523,7 +525,7 @@ const uploadVariant = async (conn, normalizedVariant) => {
     let content = {};
 
     if (normalizedVariant.positional) {
-        content = parseVariant(normalizedVariant.variant, false).toJSON();
+        content = jsonifyVariant(parseVariant(normalizedVariant.variant, false));
     }
 
     // Variant type
diff --git a/src/cosmic/resistance.js b/src/cosmic/resistance.js
index 1570830d..881b04ec 100644
--- a/src/cosmic/resistance.js
+++ b/src/cosmic/resistance.js
@@ -3,10 +3,7 @@
  */
 const fs = require('fs');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     loadDelimToJson,
@@ -80,7 +77,7 @@ const processVariants = async ({ conn, record, source }) => {
 
     try {
         // add the protein variant with its protein translation
-        const variant = parseVariant(record.protein, false).toJSON();
+        const variant = jsonifyVariant(parseVariant(record.protein, false));
         variant.type = rid(await conn.getVocabularyTerm(variant.type));
 
         const reference1 = rid(await _ensembl.fetchAndLoadById(
@@ -116,7 +113,7 @@ const processVariants = async ({ conn, record, source }) => {
     // create the cds variant
     if (record.cds && record.cds.trim()) {
         try {
-            const variant = parseVariant(record.cds, false).toJSON();
+            const variant = jsonifyVariant(parseVariant(record.cds, false));
             // get the ensembl transcript
             const reference1 = rid(await _ensembl.fetchAndLoadById(
                 conn,
@@ -146,7 +143,7 @@ const processVariants = async ({ conn, record, source }) => {
     // add the genomic representation
     if (record.genomic) {
         try {
-            const variant = parseVariant(record.genomic, false).toJSON();
+            const variant = jsonifyVariant(parseVariant(record.genomic, false));
             // get the chromosome
             const reference1 = rid(await conn.getUniqueRecordBy({
                 filters: {
diff --git a/src/docm/index.js b/src/docm/index.js
index 08732105..c4693ee2 100644
--- a/src/docm/index.js
+++ b/src/docm/index.js
@@ -6,10 +6,7 @@
 const Ajv = require('ajv');
 const fs = require('fs');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const { checkSpec, request } = require('../util');
 const {
@@ -110,7 +107,7 @@ const processVariants = async ({ conn, source, record: docmRecord }) => {
     try {
         // create the protein variant
         const [reference1] = await _gene.fetchAndLoadBySymbol(conn, gene);
-        let variant = parseVariant(parseDocmVariant(aminoAcid), false).toJSON();
+        let variant = jsonifyVariant(parseVariant(parseDocmVariant(aminoAcid), false));
         const type = await conn.getVocabularyTerm(variant.type);
         protein = variant = await conn.addVariant({
             content: { ...variant, reference1: rid(reference1), type: rid(type) },
@@ -124,7 +121,7 @@ const processVariants = async ({ conn, source, record: docmRecord }) => {
 
     try {
         // create the genomic variant
-        let variant = parseVariant(buildGenomicVariant(docmRecord), false).toJSON();
+        let variant = jsonifyVariant(parseVariant(buildGenomicVariant(docmRecord), false));
         const type = await conn.getVocabularyTerm(variant.type);
         const reference1 = await conn.getUniqueRecordBy({
             filters: {
diff --git a/src/entrez/snp.js b/src/entrez/snp.js
index 362ac3f4..5d17d279 100644
--- a/src/entrez/snp.js
+++ b/src/entrez/snp.js
@@ -1,6 +1,6 @@
 const Ajv = require('ajv');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 const { checkSpec } = require('../util');
 const {
     fetchByIdList, uploadRecord, preLoadCache: preLoadAnyCache, BASE_FETCH_URL,
@@ -10,10 +10,6 @@ const entrezGene = require('./gene');
 const { rid } = require('../graphkb');
 const { logger } = require('../logging');
 
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
-
 const ajv = new Ajv();
 
 const { dbSnp: SOURCE_DEFN } = require('../sources');
@@ -52,7 +48,7 @@ const loadFromDocsumHgvs = async (api, hgvsVariants) => {
 
     try {
         if (hgvsVariants.cds) {
-            const parsed = parseVariant(hgvsVariants.cds.split('|')[0], true).toJSON();
+            const parsed = jsonifyVariant(parseVariant(hgvsVariants.cds.split('|')[0], true));
             const [transcript] = await refseq.fetchAndLoadByIds(api, [parsed.reference1]);
             const type = await api.getVocabularyTerm(parsed.type);
             cds = await api.addVariant({
@@ -68,7 +64,7 @@ const loadFromDocsumHgvs = async (api, hgvsVariants) => {
     try {
         if (hgvsVariants.protein) {
             const gene = hgvsVariants.protein.split('|').find(p => p.startsWith('GENE='));
-            const parsed = parseVariant(hgvsVariants.protein.split('|')[0], true).toJSON();
+            const parsed = jsonifyVariant(parseVariant(hgvsVariants.protein.split('|')[0], true));
             const [reference1] = await refseq.fetchAndLoadByIds(api, [parsed.reference1]);
             const type = await api.getVocabularyTerm(parsed.type);
             protein = await api.addVariant({
diff --git a/src/moa/index.js b/src/moa/index.js
index df50c4d1..1ba0fd31 100644
--- a/src/moa/index.js
+++ b/src/moa/index.js
@@ -1,9 +1,6 @@
 const Ajv = require('ajv');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 
 const { checkSpec, requestWithRetry } = require('../util');
 const { moa: SOURCE_DEFN } = require('../sources');
@@ -62,7 +59,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the genomic variant if we have the appropriate fields
     if (!['reference_allele', 'alternate_allele', 'start_position', 'end_position', 'chromosome'].some(v => moaVariant[v] === null)) {
-        const hgvsg = parseVariant(composeGenomicHgvs(moaVariant), false).toJSON();
+        const hgvsg = jsonifyVariant(parseVariant(composeGenomicHgvs(moaVariant), false));
         const chromosome = await conn.getUniqueRecordBy({
             filters: {
                 AND: [
@@ -88,7 +85,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the cds variant
     if (moaVariant.cdna_change !== null && moaVariant.cdna_change !== '') {
-        const hgvsc = parseVariant(moaVariant.cdna_change, false).toJSON();
+        const hgvsc = jsonifyVariant(parseVariant(moaVariant.cdna_change, false));
         const cdsType = rid(await conn.getVocabularyTerm(hgvsc.type));
         cdsVariant = rid(await conn.addVariant({
             content: {
@@ -101,7 +98,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
 
     // create the protein variant
     if (moaVariant.protein_change !== null && moaVariant.protein_change !== '') {
-        const hgvsp = parseVariant(moaVariant.protein_change, false).toJSON();
+        const hgvsp = jsonifyVariant(parseVariant(moaVariant.protein_change, false));
         const proteinType = rid(await conn.getVocabularyTerm(hgvsp.type));
         proteinVariant = rid(await conn.addVariant({
             content: {
@@ -132,7 +129,7 @@ const loadSmallMutation = async (conn, gene, moaVariant) => {
         } else {
             variantType = await conn.getVocabularyTerm('mutation');
         }
-        const parsed = parseVariant(`e.${exonNumber}mut`, false).toJSON();
+        const parsed = jsonifyVariant(parseVariant(`e.${exonNumber}mut`, false));
         exonVariant = await conn.addVariant({
             content: {
                 ...parsed,
diff --git a/src/oncokb/index.js b/src/oncokb/index.js
index a6498496..2d132ba6 100644
--- a/src/oncokb/index.js
+++ b/src/oncokb/index.js
@@ -5,10 +5,7 @@ const Ajv = require('ajv');
 const fs = require('fs');
 const path = require('path');
 
-const { ParsingError, parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
+const { jsonifyVariant, parseVariant, ParsingError } = require('@bcgsc-pori/graphkb-parser');
 
 const {
     checkSpec,
@@ -279,11 +276,11 @@ const processVariant = async (conn, {
 
     if (!variant) {
         try {
-            variant = parseVariant(type, false).toJSON();
+            variant = jsonifyVariant(parseVariant(type, false));
         } catch (err) {
             try {
                 // try with adding a p prefix also
-                variant = parseVariant(`p.${type}`, false).toJSON();
+                variant = jsonifyVariant(parseVariant(`p.${type}`, false));
             } catch (err2) { }
             logger.warn(`failed to parse the variant (${type}) for record (gene=${gene}, variant=${variantName})`);
             throw err;
@@ -330,7 +327,7 @@ const processVariant = async (conn, {
 
         try {
             // try with adding a p prefix also
-            const parsed = parseVariant(altVariantName, false).toJSON();
+            const parsed = jsonifyVariant(parseVariant(altVariantName, false));
             parsed.reference1 = rid(reference1);
             parsed.type = rid(await getVocabulary(conn, parsed.type));
             const altVariant = rid(await conn.addVariant({
diff --git a/src/util.js b/src/util.js
index 32238712..0a4a6823 100644
--- a/src/util.js
+++ b/src/util.js
@@ -225,49 +225,6 @@ const convertRowFields = (header, row) => {
     return result;
 };
 
-/**
- * Decorator function to add toJSON() method to parseVariant returned object
- * (from graphkb-parser v1 not avail. anymore in v2.1.1)
- */
-function parseVariantDecorator(parseVariant) {
-    // Method
-    function toJSON() {
-        const positionToJSON = (position) => {
-            const json = {};
-
-            for (const [attr, value] of Object.entries(position)) {
-                if (value !== null && !['prefix', 'longRefAA'].includes(attr)) {
-                    json[attr] = value;
-                }
-            }
-            return json;
-        };
-
-        const json = {};
-        const IGNORE = ['prefix', 'multiFeature', 'noFeatures', 'notationType', 'toJSON'];
-
-        for (const [attr, value] of Object.entries(this)) {
-            if (value !== undefined && !IGNORE.includes(attr)) {
-                if (value.pos) {
-                    json[attr] = positionToJSON(value);
-                } else {
-                    json[attr] = value;
-                }
-            }
-        }
-        return json;
-    }
-
-    return function (...args) {
-        const result = parseVariant(...args);
-
-        if (!('toJSON' in result) || typeof result.toJSON !== 'function') {
-            result.toJSON = toJSON;
-        }
-        return result;
-    };
-}
-
 
 module.exports = {
     checkSpec,
@@ -278,7 +235,6 @@ module.exports = {
     loadDelimToJson,
     loadXmlToJson,
     logger,
-    parseVariantDecorator,
     parseXmlToJson,
     request,
     requestWithRetry,
diff --git a/src/variants/index.js b/src/variants/index.js
index c2aa2a52..8b20c575 100644
--- a/src/variants/index.js
+++ b/src/variants/index.js
@@ -1,14 +1,10 @@
 const fs = require('fs');
 
-const { parseVariant: parseVariantOriginal } = require('@bcgsc-pori/graphkb-parser');
+const { jsonifyVariant, parseVariant } = require('@bcgsc-pori/graphkb-parser');
 const { logger } = require('../logging');
 const { orderPreferredOntologyTerms, rid } = require('../graphkb');
 const { fetchAndLoadBySymbol } = require('../entrez/gene');
 
-const { parseVariantDecorator } = require('../util');
-
-const parseVariant = parseVariantDecorator(parseVariantOriginal);
-
 
 const getEntrezGene = async (conn, name) => {
     try {
@@ -51,7 +47,7 @@ const uploadFile = async (opt) => {
         logger.info(`loading ${variant}`);
 
         try {
-            const parsed = parseVariant(variant, true).toJSON();
+            const parsed = jsonifyVariant(parseVariant(variant, true));
             const variantType = await conn.getVocabularyTerm(parsed.type);
             const reference1 = await getEntrezGene(conn, parsed.reference1);
 

From 0ecad9a757a7f1e3e3ed42bff6f54bba68e49185 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 13:25:23 -0800
Subject: [PATCH 16/29] npm audit fix --force w/ node v16.20.2

---
 package-lock.json | 698 ++++++++++++++++++++++++++++++++++------------
 package.json      |   6 +-
 2 files changed, 522 insertions(+), 182 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 4e380348..6726e830 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -20,7 +20,7 @@
         "json-cycle": "^1.3.0",
         "json-stable-stringify": "^1.0.1",
         "jsonpath": "^1.1.1",
-        "jsonwebtoken": "^8.5.1",
+        "jsonwebtoken": "^9.0.2",
         "lodash": "^4.17.21",
         "node-expat": "^2.3.18",
         "node-fetch": "^2.6.7",
@@ -31,13 +31,13 @@
         "sleep-promise": "^8.0.1",
         "winston": "^3.2.1",
         "xml-stream": "^0.4.5",
-        "xml2js": "^0.4.19"
+        "xml2js": "^0.6.2"
       },
       "devDependencies": {
         "eslint": "^8.17.0",
         "eslint-config-airbnb": "^19.0.4",
         "eslint-plugin-import": "^2.26.0",
-        "eslint-plugin-jest": "^22.20.0",
+        "eslint-plugin-jest": "^28.10.0",
         "eslint-plugin-jest-formatting": "^1.1.0",
         "eslint-plugin-jsx-a11y": "^6.5.1",
         "eslint-plugin-react": "^7.30.0",
@@ -658,6 +658,24 @@
         "node": ">=10.0.0"
       }
     },
+    "node_modules/@eslint-community/eslint-utils": {
+      "version": "4.4.1",
+      "resolved": "https://registry.npmjs.org/@eslint-community/eslint-utils/-/eslint-utils-4.4.1.tgz",
+      "integrity": "sha512-s3O3waFUrMV8P/XaF/+ZTp1X9XBZW1a4B97ZnjQF2KYWaFD2A8KyFBsrsfSjEmjn3RGWAIuvlneuZm3CUK3jbA==",
+      "dev": true,
+      "dependencies": {
+        "eslint-visitor-keys": "^3.4.3"
+      },
+      "engines": {
+        "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+      },
+      "funding": {
+        "url": "https://opencollective.com/eslint"
+      },
+      "peerDependencies": {
+        "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
+      }
+    },
     "node_modules/@eslint/eslintrc": {
       "version": "1.3.0",
       "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-1.3.0.tgz",
@@ -2112,6 +2130,41 @@
         "@jridgewell/sourcemap-codec": "^1.4.14"
       }
     },
+    "node_modules/@nodelib/fs.scandir": {
+      "version": "2.1.5",
+      "resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.5.tgz",
+      "integrity": "sha512-vq24Bq3ym5HEQm2NKCr3yXDwjc7vTsEThRDnkp2DK9p1uqLR+DHurm/NOTo0KG7HYHU7eppKZj3MyqYuMBf62g==",
+      "dev": true,
+      "dependencies": {
+        "@nodelib/fs.stat": "2.0.5",
+        "run-parallel": "^1.1.9"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
+    "node_modules/@nodelib/fs.stat": {
+      "version": "2.0.5",
+      "resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-2.0.5.tgz",
+      "integrity": "sha512-RkhPPp2zrqDAQA/2jNhnztcPAlv64XdhIp7a7454A5ovI7Bukxgt7MX7udwAu3zg1DcpPU0rz3VV1SeaqvY4+A==",
+      "dev": true,
+      "engines": {
+        "node": ">= 8"
+      }
+    },
+    "node_modules/@nodelib/fs.walk": {
+      "version": "1.2.8",
+      "resolved": "https://registry.npmjs.org/@nodelib/fs.walk/-/fs.walk-1.2.8.tgz",
+      "integrity": "sha512-oGB+UxlgWcgQkgwo8GcEGwemoTFt3FIO9ababBmaGwXIoBKZ+GTy0pP185beGg7Llih/NSHSV2XAs1lnznocSg==",
+      "dev": true,
+      "dependencies": {
+        "@nodelib/fs.scandir": "2.1.5",
+        "fastq": "^1.6.0"
+      },
+      "engines": {
+        "node": ">= 8"
+      }
+    },
     "node_modules/@sinonjs/commons": {
       "version": "1.8.3",
       "resolved": "https://registry.npmjs.org/@sinonjs/commons/-/commons-1.8.3.tgz",
@@ -2204,12 +2257,6 @@
         "@types/istanbul-lib-coverage": "*"
       }
     },
-    "node_modules/@types/json-schema": {
-      "version": "7.0.3",
-      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.3.tgz",
-      "integrity": "sha512-Il2DtDVRGDcqjDtE+rF8iqg1CArehSK84HZJCT7AMITlyXRBpuPhqGLDQMowraqqu1coEaimg4ZOqggt6L6L+A==",
-      "dev": true
-    },
     "node_modules/@types/json5": {
       "version": "0.0.29",
       "resolved": "https://registry.npmjs.org/@types/json5/-/json5-0.0.29.tgz",
@@ -2240,43 +2287,113 @@
       "integrity": "sha512-7tFImggNeNBVMsn0vLrpn1H1uPrUBdnARPTpZoitY37ZrdJREzf7I16tMrlK3hen349gr1NYh8CmZQa7CTG6Aw==",
       "dev": true
     },
-    "node_modules/@typescript-eslint/experimental-utils": {
-      "version": "1.13.0",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/experimental-utils/-/experimental-utils-1.13.0.tgz",
-      "integrity": "sha512-zmpS6SyqG4ZF64ffaJ6uah6tWWWgZ8m+c54XXgwFtUv0jNz8aJAVx8chMCvnk7yl6xwn8d+d96+tWp7fXzTuDg==",
+    "node_modules/@typescript-eslint/scope-manager": {
+      "version": "8.19.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-8.19.0.tgz",
+      "integrity": "sha512-hkoJiKQS3GQ13TSMEiuNmSCvhz7ujyqD1x3ShbaETATHrck+9RaDdUbt+osXaUuns9OFwrDTTrjtwsU8gJyyRA==",
       "dev": true,
       "dependencies": {
-        "@types/json-schema": "^7.0.3",
-        "@typescript-eslint/typescript-estree": "1.13.0",
-        "eslint-scope": "^4.0.0"
+        "@typescript-eslint/types": "8.19.0",
+        "@typescript-eslint/visitor-keys": "8.19.0"
       },
       "engines": {
-        "node": "^6.14.0 || ^8.10.0 || >=9.10.0"
+        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
       },
-      "peerDependencies": {
-        "eslint": "*"
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/typescript-eslint"
+      }
+    },
+    "node_modules/@typescript-eslint/types": {
+      "version": "8.19.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-8.19.0.tgz",
+      "integrity": "sha512-8XQ4Ss7G9WX8oaYvD4OOLCjIQYgRQxO+qCiR2V2s2GxI9AUpo7riNwo6jDhKtTcaJjT8PY54j2Yb33kWtSJsmA==",
+      "dev": true,
+      "engines": {
+        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/typescript-eslint"
       }
     },
     "node_modules/@typescript-eslint/typescript-estree": {
-      "version": "1.13.0",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-1.13.0.tgz",
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+      "version": "8.19.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-8.19.0.tgz",
+      "integrity": "sha512-WW9PpDaLIFW9LCbucMSdYUuGeFUz1OkWYS/5fwZwTA+l2RwlWFdJvReQqMUMBw4yJWJOfqd7An9uwut2Oj8sLw==",
       "dev": true,
       "dependencies": {
-        "lodash.unescape": "4.0.1",
-        "semver": "5.5.0"
+        "@typescript-eslint/types": "8.19.0",
+        "@typescript-eslint/visitor-keys": "8.19.0",
+        "debug": "^4.3.4",
+        "fast-glob": "^3.3.2",
+        "is-glob": "^4.0.3",
+        "minimatch": "^9.0.4",
+        "semver": "^7.6.0",
+        "ts-api-utils": "^1.3.0"
       },
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+        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
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+        "type": "opencollective",
+        "url": "https://opencollective.com/typescript-eslint"
+      },
+      "peerDependencies": {
+        "typescript": ">=4.8.4 <5.8.0"
       }
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-    "node_modules/@typescript-eslint/typescript-estree/node_modules/semver": {
-      "version": "5.5.0",
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+    "node_modules/@typescript-eslint/typescript-estree/node_modules/brace-expansion": {
+      "version": "2.0.1",
+      "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz",
+      "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==",
       "dev": true,
-      "bin": {
-        "semver": "bin/semver"
+      "dependencies": {
+        "balanced-match": "^1.0.0"
+      }
+    },
+    "node_modules/@typescript-eslint/typescript-estree/node_modules/minimatch": {
+      "version": "9.0.5",
+      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.5.tgz",
+      "integrity": "sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow==",
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+      "dependencies": {
+        "brace-expansion": "^2.0.1"
+      },
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+      },
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+      "version": "8.19.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-8.19.0.tgz",
+      "integrity": "sha512-mCFtBbFBJDCNCWUl5y6sZSCHXw1DEFEk3c/M3nRK2a4XUB8StGFtmcEMizdjKuBzB6e/smJAAWYug3VrdLMr1w==",
+      "dev": true,
+      "dependencies": {
+        "@typescript-eslint/types": "8.19.0",
+        "eslint-visitor-keys": "^4.2.0"
+      },
+      "engines": {
+        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/typescript-eslint"
+      }
+    },
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@@ -20406,6 +20732,13 @@
       "resolved": "https://registry.npmjs.org/triple-beam/-/triple-beam-1.3.0.tgz",
       "integrity": "sha512-XrHUvV5HpdLmIj4uVMxHggLbFSZYIn7HEWsqePZcI50pco+MPqJ50wMGY794X7AOOhxOBAjbkqfAbEe/QMp2Lw=="
     },
+    "ts-api-utils": {
+      "version": "1.4.3",
+      "resolved": "https://registry.npmjs.org/ts-api-utils/-/ts-api-utils-1.4.3.tgz",
+      "integrity": "sha512-i3eMG77UTMD0hZhgRS562pv83RC6ukSAC2GMNWc+9dieh/+jDM5u5YG+NHX6VNDRHQcHwmsTHctP9LhbC3WxVw==",
+      "dev": true,
+      "requires": {}
+    },
     "tsconfig-paths": {
       "version": "3.14.1",
       "resolved": "https://registry.npmjs.org/tsconfig-paths/-/tsconfig-paths-3.14.1.tgz",
@@ -20458,6 +20791,13 @@
         "is-typedarray": "^1.0.0"
       }
     },
+    "typescript": {
+      "version": "5.7.2",
+      "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.7.2.tgz",
+      "integrity": "sha512-i5t66RHxDvVN40HfDd1PsEThGNnlMCMT3jMUuoh9/0TaqWevNontacunWyN02LA9/fIbEWlcHZcgTKb9QoaLfg==",
+      "dev": true,
+      "peer": true
+    },
     "unbox-primitive": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/unbox-primitive/-/unbox-primitive-1.0.2.tgz",
@@ -20875,9 +21215,9 @@
       }
     },
     "xml2js": {
-      "version": "0.4.23",
-      "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.4.23.tgz",
-      "integrity": "sha512-ySPiMjM0+pLDftHgXY4By0uswI3SPKLDw/i3UXbnO8M/p28zqexCUoPmQFrYD+/1BzhGJSs2i1ERWKJAtiLrug==",
+      "version": "0.6.2",
+      "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz",
+      "integrity": "sha512-T4rieHaC1EXcES0Kxxj4JWgaUQHDk+qwHcYOCFHfiwKz7tOVPLq7Hjq9dM1WCMhylqMEfP7hMcOIChvotiZegA==",
       "requires": {
         "sax": ">=0.6.0",
         "xmlbuilder": "~11.0.0"
diff --git a/package.json b/package.json
index 4ef77ca7..95922f8c 100644
--- a/package.json
+++ b/package.json
@@ -23,7 +23,7 @@
     "json-cycle": "^1.3.0",
     "json-stable-stringify": "^1.0.1",
     "jsonpath": "^1.1.1",
-    "jsonwebtoken": "^8.5.1",
+    "jsonwebtoken": "^9.0.2",
     "lodash": "^4.17.21",
     "node-expat": "^2.3.18",
     "node-fetch": "^2.6.7",
@@ -34,13 +34,13 @@
     "sleep-promise": "^8.0.1",
     "winston": "^3.2.1",
     "xml-stream": "^0.4.5",
-    "xml2js": "^0.4.19"
+    "xml2js": "^0.6.2"
   },
   "devDependencies": {
     "eslint": "^8.17.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-plugin-import": "^2.26.0",
-    "eslint-plugin-jest": "^22.20.0",
+    "eslint-plugin-jest": "^28.10.0",
     "eslint-plugin-jest-formatting": "^1.1.0",
     "eslint-plugin-jsx-a11y": "^6.5.1",
     "eslint-plugin-react": "^7.30.0",

From 357794a2d134af9ff266c5811cef8b2c1d9882b0 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 13:43:59 -0800
Subject: [PATCH 17/29] Override iconv version for xml-stream

---
 package-lock.json | 30 +++++++++++++++---------------
 package.json      |  5 +++++
 2 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 6726e830..cfe89c84 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -5245,12 +5245,12 @@
       }
     },
     "node_modules/iconv": {
-      "version": "2.3.4",
-      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.4.tgz",
-      "integrity": "sha512-v2Rree7xRtrC9o3Bi9nTNOKXvApmwLFdX50k72+K1W4mJ93LBdpaLcHcInYo9gr/GcQk8MFoCetrYRcb/o3RLg==",
+      "version": "2.3.5",
+      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.5.tgz",
+      "integrity": "sha512-U5ajDbtDfadp7pvUMC0F2XbkP5vQn9Xrwa6UptePl+cK8EILxapAt3sXers9B3Gxagk+zVjL2ELKuzQvyqOwug==",
       "hasInstallScript": true,
       "dependencies": {
-        "nan": "^2.13.1",
+        "nan": "^2.14.0",
         "safer-buffer": "^2.1.2"
       },
       "engines": {
@@ -10131,9 +10131,9 @@
       }
     },
     "node_modules/nan": {
-      "version": "2.13.2",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.13.2.tgz",
-      "integrity": "sha512-TghvYc72wlMGMVMluVo9WRJc0mB8KxxF/gZ4YYFy7V2ZQX9l7rgbPg7vjS9mt6U5HXODVFVI2bOduCzwOMv/lw=="
+      "version": "2.22.0",
+      "resolved": "https://registry.npmjs.org/nan/-/nan-2.22.0.tgz",
+      "integrity": "sha512-nbajikzWTMwsW+eSsNm3QwlOs7het9gGJU5dDZzRTQGk03vyBOauxgI4VakDzE0PtsGTmXPsXTbbjVhRwR5mpw=="
     },
     "node_modules/natural-compare": {
       "version": "1.4.0",
@@ -16038,11 +16038,11 @@
       "dev": true
     },
     "iconv": {
-      "version": "2.3.4",
-      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.4.tgz",
-      "integrity": "sha512-v2Rree7xRtrC9o3Bi9nTNOKXvApmwLFdX50k72+K1W4mJ93LBdpaLcHcInYo9gr/GcQk8MFoCetrYRcb/o3RLg==",
+      "version": "2.3.5",
+      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.5.tgz",
+      "integrity": "sha512-U5ajDbtDfadp7pvUMC0F2XbkP5vQn9Xrwa6UptePl+cK8EILxapAt3sXers9B3Gxagk+zVjL2ELKuzQvyqOwug==",
       "requires": {
-        "nan": "^2.13.1",
+        "nan": "^2.14.0",
         "safer-buffer": "^2.1.2"
       }
     },
@@ -19822,9 +19822,9 @@
       }
     },
     "nan": {
-      "version": "2.13.2",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.13.2.tgz",
-      "integrity": "sha512-TghvYc72wlMGMVMluVo9WRJc0mB8KxxF/gZ4YYFy7V2ZQX9l7rgbPg7vjS9mt6U5HXODVFVI2bOduCzwOMv/lw=="
+      "version": "2.22.0",
+      "resolved": "https://registry.npmjs.org/nan/-/nan-2.22.0.tgz",
+      "integrity": "sha512-nbajikzWTMwsW+eSsNm3QwlOs7het9gGJU5dDZzRTQGk03vyBOauxgI4VakDzE0PtsGTmXPsXTbbjVhRwR5mpw=="
     },
     "natural-compare": {
       "version": "1.4.0",
@@ -21186,7 +21186,7 @@
       "resolved": "https://registry.npmjs.org/xml-stream/-/xml-stream-0.4.5.tgz",
       "integrity": "sha1-dFLYWzf5uIGnDv8M90oN8CCI7es=",
       "requires": {
-        "iconv": "^2.1.4",
+        "iconv": "2.3.5",
         "node-expat": "^2.3.1",
         "readable-stream": "^1.0.31"
       },
diff --git a/package.json b/package.json
index 95922f8c..7e7ad5f2 100644
--- a/package.json
+++ b/package.json
@@ -52,6 +52,11 @@
     "jest-circus": "^27.3.1",
     "jest-junit": "^13.0.0"
   },
+  "overrides": {
+    "xml-stream": {
+      "iconv": "2.3.5"
+    }
+  },
   "scripts": {
     "test": "NODE_ENV=test jest --config config/jest.config.js",
     "lint": "eslint -c .eslintrc.json src test",

From e212058c1863c295f5eba60bbe953c9c9b44ae80 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:22:17 -0800
Subject: [PATCH 18/29] remove xml-stream and temp. deactivate drugbank loader

---
 package-lock.json     | 133 ++++++++++++++----------------------------
 package.json          |   7 +--
 src/drugbank/index.js | 116 ++++++++++++++++++------------------
 test/loadfile.test.js |   2 +-
 4 files changed, 104 insertions(+), 154 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index cfe89c84..100a44d4 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -15,6 +15,7 @@
         "argparse": "^2.0.1",
         "csv-parse": "^4.6.5",
         "fast-csv": "^4.3.6",
+        "fast-xml-parser": "^4.5.1",
         "html-to-text": "^5.1.1",
         "http-status-codes": "^1.3.2",
         "json-cycle": "^1.3.0",
@@ -30,7 +31,6 @@
         "read-excel-file": "^5.2.28",
         "sleep-promise": "^8.0.1",
         "winston": "^3.2.1",
-        "xml-stream": "^0.4.5",
         "xml2js": "^0.6.2"
       },
       "devDependencies": {
@@ -4688,6 +4688,27 @@
       "resolved": "https://registry.npmjs.org/fast-safe-stringify/-/fast-safe-stringify-2.0.6.tgz",
       "integrity": "sha512-q8BZ89jjc+mz08rSxROs8VsrBBcn1SIw1kq9NjolL509tkABRk9io01RAjSaEv1Xb2uFLt8VtRiZbGp5H8iDtg=="
     },
+    "node_modules/fast-xml-parser": {
+      "version": "4.5.1",
+      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.5.1.tgz",
+      "integrity": "sha512-y655CeyUQ+jj7KBbYMc4FG01V8ZQqjN+gDYGJ50RtfsUB8iG9AmwmwoAgeKLJdmueKKMrH1RJ7yXHTSoczdv5w==",
+      "funding": [
+        {
+          "type": "github",
+          "url": "https://github.com/sponsors/NaturalIntelligence"
+        },
+        {
+          "type": "paypal",
+          "url": "https://paypal.me/naturalintelligence"
+        }
+      ],
+      "dependencies": {
+        "strnum": "^1.0.5"
+      },
+      "bin": {
+        "fxparser": "src/cli/cli.js"
+      }
+    },
     "node_modules/fastq": {
       "version": "1.18.0",
       "resolved": "https://registry.npmjs.org/fastq/-/fastq-1.18.0.tgz",
@@ -5244,19 +5265,6 @@
         "node": ">=10.17.0"
       }
     },
-    "node_modules/iconv": {
-      "version": "2.3.5",
-      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.5.tgz",
-      "integrity": "sha512-U5ajDbtDfadp7pvUMC0F2XbkP5vQn9Xrwa6UptePl+cK8EILxapAt3sXers9B3Gxagk+zVjL2ELKuzQvyqOwug==",
-      "hasInstallScript": true,
-      "dependencies": {
-        "nan": "^2.14.0",
-        "safer-buffer": "^2.1.2"
-      },
-      "engines": {
-        "node": ">=0.8.0"
-      }
-    },
     "node_modules/iconv-lite": {
       "version": "0.4.24",
       "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.24.tgz",
@@ -10839,7 +10847,8 @@
     "node_modules/safer-buffer": {
       "version": "2.1.2",
       "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz",
-      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
+      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==",
+      "dev": true
     },
     "node_modules/sax": {
       "version": "1.2.4",
@@ -11129,6 +11138,11 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/strnum": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/strnum/-/strnum-1.0.5.tgz",
+      "integrity": "sha512-J8bbNyKKXl5qYcR36TIO8W3mVGVHrmmxsd5PAItGkmyzwJvybiw2IVq5nqd0i4LSNSkB/sx9VHllbfFdr9k1JA=="
+    },
     "node_modules/supports-color": {
       "version": "5.5.0",
       "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-5.5.0.tgz",
@@ -11867,37 +11881,6 @@
       "integrity": "sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw==",
       "dev": true
     },
-    "node_modules/xml-stream": {
-      "version": "0.4.5",
-      "resolved": "https://registry.npmjs.org/xml-stream/-/xml-stream-0.4.5.tgz",
-      "integrity": "sha1-dFLYWzf5uIGnDv8M90oN8CCI7es=",
-      "dependencies": {
-        "iconv": "^2.1.4",
-        "node-expat": "^2.3.1",
-        "readable-stream": "^1.0.31"
-      }
-    },
-    "node_modules/xml-stream/node_modules/isarray": {
-      "version": "0.0.1",
-      "resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz",
-      "integrity": "sha1-ihis/Kmo9Bd+Cav8YDiTmwXR7t8="
-    },
-    "node_modules/xml-stream/node_modules/readable-stream": {
-      "version": "1.1.14",
-      "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.1.14.tgz",
-      "integrity": "sha1-fPTFTvZI44EwhMY23SB54WbAgdk=",
-      "dependencies": {
-        "core-util-is": "~1.0.0",
-        "inherits": "~2.0.1",
-        "isarray": "0.0.1",
-        "string_decoder": "~0.10.x"
-      }
-    },
-    "node_modules/xml-stream/node_modules/string_decoder": {
-      "version": "0.10.31",
-      "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
-      "integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
-    },
     "node_modules/xml2js": {
       "version": "0.6.2",
       "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz",
@@ -15633,6 +15616,14 @@
       "resolved": "https://registry.npmjs.org/fast-safe-stringify/-/fast-safe-stringify-2.0.6.tgz",
       "integrity": "sha512-q8BZ89jjc+mz08rSxROs8VsrBBcn1SIw1kq9NjolL509tkABRk9io01RAjSaEv1Xb2uFLt8VtRiZbGp5H8iDtg=="
     },
+    "fast-xml-parser": {
+      "version": "4.5.1",
+      "resolved": "https://registry.npmjs.org/fast-xml-parser/-/fast-xml-parser-4.5.1.tgz",
+      "integrity": "sha512-y655CeyUQ+jj7KBbYMc4FG01V8ZQqjN+gDYGJ50RtfsUB8iG9AmwmwoAgeKLJdmueKKMrH1RJ7yXHTSoczdv5w==",
+      "requires": {
+        "strnum": "^1.0.5"
+      }
+    },
     "fastq": {
       "version": "1.18.0",
       "resolved": "https://registry.npmjs.org/fastq/-/fastq-1.18.0.tgz",
@@ -16037,15 +16028,6 @@
       "integrity": "sha512-B4FFZ6q/T2jhhksgkbEW3HBvWIfDW85snkQgawt07S7J5QXTk6BkNV+0yAeZrM5QpMAdYlocGoljn0sJ/WQkFw==",
       "dev": true
     },
-    "iconv": {
-      "version": "2.3.5",
-      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.5.tgz",
-      "integrity": "sha512-U5ajDbtDfadp7pvUMC0F2XbkP5vQn9Xrwa6UptePl+cK8EILxapAt3sXers9B3Gxagk+zVjL2ELKuzQvyqOwug==",
-      "requires": {
-        "nan": "^2.14.0",
-        "safer-buffer": "^2.1.2"
-      }
-    },
     "iconv-lite": {
       "version": "0.4.24",
       "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.24.tgz",
@@ -20346,7 +20328,8 @@
     "safer-buffer": {
       "version": "2.1.2",
       "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz",
-      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
+      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==",
+      "dev": true
     },
     "sax": {
       "version": "1.2.4",
@@ -20577,6 +20560,11 @@
       "integrity": "sha512-6fPc+R4ihwqP6N/aIv2f1gMH8lOVtWQHoqC4yK6oSDVVocumAsfCqjkXnqiYMhmMwS/mEHLp7Vehlt3ql6lEig==",
       "dev": true
     },
+    "strnum": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/strnum/-/strnum-1.0.5.tgz",
+      "integrity": "sha512-J8bbNyKKXl5qYcR36TIO8W3mVGVHrmmxsd5PAItGkmyzwJvybiw2IVq5nqd0i4LSNSkB/sx9VHllbfFdr9k1JA=="
+    },
     "supports-color": {
       "version": "5.5.0",
       "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-5.5.0.tgz",
@@ -21181,39 +21169,6 @@
       "integrity": "sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw==",
       "dev": true
     },
-    "xml-stream": {
-      "version": "0.4.5",
-      "resolved": "https://registry.npmjs.org/xml-stream/-/xml-stream-0.4.5.tgz",
-      "integrity": "sha1-dFLYWzf5uIGnDv8M90oN8CCI7es=",
-      "requires": {
-        "iconv": "2.3.5",
-        "node-expat": "^2.3.1",
-        "readable-stream": "^1.0.31"
-      },
-      "dependencies": {
-        "isarray": {
-          "version": "0.0.1",
-          "resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz",
-          "integrity": "sha1-ihis/Kmo9Bd+Cav8YDiTmwXR7t8="
-        },
-        "readable-stream": {
-          "version": "1.1.14",
-          "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.1.14.tgz",
-          "integrity": "sha1-fPTFTvZI44EwhMY23SB54WbAgdk=",
-          "requires": {
-            "core-util-is": "~1.0.0",
-            "inherits": "~2.0.1",
-            "isarray": "0.0.1",
-            "string_decoder": "~0.10.x"
-          }
-        },
-        "string_decoder": {
-          "version": "0.10.31",
-          "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
-          "integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
-        }
-      }
-    },
     "xml2js": {
       "version": "0.6.2",
       "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz",
diff --git a/package.json b/package.json
index 7e7ad5f2..ec0a3ee2 100644
--- a/package.json
+++ b/package.json
@@ -18,6 +18,7 @@
     "argparse": "^2.0.1",
     "csv-parse": "^4.6.5",
     "fast-csv": "^4.3.6",
+    "fast-xml-parser": "^4.5.1",
     "html-to-text": "^5.1.1",
     "http-status-codes": "^1.3.2",
     "json-cycle": "^1.3.0",
@@ -33,7 +34,6 @@
     "read-excel-file": "^5.2.28",
     "sleep-promise": "^8.0.1",
     "winston": "^3.2.1",
-    "xml-stream": "^0.4.5",
     "xml2js": "^0.6.2"
   },
   "devDependencies": {
@@ -52,11 +52,6 @@
     "jest-circus": "^27.3.1",
     "jest-junit": "^13.0.0"
   },
-  "overrides": {
-    "xml-stream": {
-      "iconv": "2.3.5"
-    }
-  },
   "scripts": {
     "test": "NODE_ENV=test jest --config config/jest.config.js",
     "lint": "eslint -c .eslintrc.json src test",
diff --git a/src/drugbank/index.js b/src/drugbank/index.js
index d3a37904..7ce2d007 100644
--- a/src/drugbank/index.js
+++ b/src/drugbank/index.js
@@ -4,7 +4,7 @@
  */
 
 const Ajv = require('ajv');
-const XmlStream = require('xml-stream');
+// const XmlStream = require('xml-stream');
 const fs = require('fs');
 
 const { checkSpec } = require('../util');
@@ -276,63 +276,63 @@ const uploadFile = async ({ filename, conn, maxRecords }) => {
     await _chembl.preLoadCache(conn);
     const counts = { error: 0, skipped: 0, success: 0 };
 
-    const parseXML = new Promise((resolve, reject) => {
-        logger.log('info', `loading XML data from ${filename}`);
-        const stream = fs.createReadStream(filename);
-        const xml = new XmlStream(stream);
-        xml.collect('drug drugbank-id');
-        xml.collect('drug external-identifier');
-        xml.collect('drug synonym');
-        xml.collect('drug categories > category');
-        xml.collect('drug atc-code level');
-        xml.collect('drug target polypeptide');
-        xml.collect('drug target actions action');
-        xml.collect('drug products product');
-        xml.collect('drug calculated-properties property');
-        xml.on('endElement: drug', (item) => {
-            if (Object.keys(item).length < 3) {
-                return;
-            }
-            xml.pause();
-            processRecord({
-                ATC, conn, drug: item, sources: { current: source, fda: fdaSource },
-            }).then(() => {
-                counts.success++;
-
-                if (maxRecords && (counts.success + counts.error + counts.skipped) >= maxRecords) {
-                    logger.warn(`not loading all content due to max records limit (${maxRecords})`);
-                    logger.info('Parsing stream complete');
-                    stream.close();
-                    resolve();
-                }
-
-                xml.resume();
-            }).catch((err) => {
-                let label;
-
-                try {
-                    label = getDrugBankId(item);
-                } catch (err2) {}  // eslint-disable-line
-                counts.error++;
-                logger.error(err);
-                logger.error(`Unable to process record ${label}`);
-                xml.resume();
-            });
-        });
-        xml.on('end', () => {
-            logger.info('Parsing stream complete');
-            stream.close();
-            resolve();
-        });
-        xml.on('error', (err) => {
-            logger.error('Parsing stream error');
-            logger.error(err);
-            stream.close();
-            reject(err);
-        });
-    });
-
-    await parseXML;
+    // const parseXML = new Promise((resolve, reject) => {
+    //     logger.log('info', `loading XML data from ${filename}`);
+    //     const stream = fs.createReadStream(filename);
+    //     const xml = new XmlStream(stream);
+    //     xml.collect('drug drugbank-id');
+    //     xml.collect('drug external-identifier');
+    //     xml.collect('drug synonym');
+    //     xml.collect('drug categories > category');
+    //     xml.collect('drug atc-code level');
+    //     xml.collect('drug target polypeptide');
+    //     xml.collect('drug target actions action');
+    //     xml.collect('drug products product');
+    //     xml.collect('drug calculated-properties property');
+    //     xml.on('endElement: drug', (item) => {
+    //         if (Object.keys(item).length < 3) {
+    //             return;
+    //         }
+    //         xml.pause();
+    //         processRecord({
+    //             ATC, conn, drug: item, sources: { current: source, fda: fdaSource },
+    //         }).then(() => {
+    //             counts.success++;
+
+    //             if (maxRecords && (counts.success + counts.error + counts.skipped) >= maxRecords) {
+    //                 logger.warn(`not loading all content due to max records limit (${maxRecords})`);
+    //                 logger.info('Parsing stream complete');
+    //                 stream.close();
+    //                 resolve();
+    //             }
+
+    //             xml.resume();
+    //         }).catch((err) => {
+    //             let label;
+
+    //             try {
+    //                 label = getDrugBankId(item);
+    //             } catch (err2) {}  // eslint-disable-line
+    //             counts.error++;
+    //             logger.error(err);
+    //             logger.error(`Unable to process record ${label}`);
+    //             xml.resume();
+    //         });
+    //     });
+    //     xml.on('end', () => {
+    //         logger.info('Parsing stream complete');
+    //         stream.close();
+    //         resolve();
+    //     });
+    //     xml.on('error', (err) => {
+    //         logger.error('Parsing stream error');
+    //         logger.error(err);
+    //         stream.close();
+    //         reject(err);
+    //     });
+    // });
+
+    // await parseXML;
     logger.log('info', JSON.stringify(counts));
 };
 
diff --git a/test/loadfile.test.js b/test/loadfile.test.js
index 7d53dddb..2b8ae27d 100644
--- a/test/loadfile.test.js
+++ b/test/loadfile.test.js
@@ -34,7 +34,7 @@ describe('diseaseOntology', () => {
 });
 
 describe('drugBank', () => {
-    test('uploadFile', async () => {
+    test.skip('uploadFile', async () => {
         const filename = path.join(__dirname, 'data/drugbank_sample.xml');
         await drugbank.uploadFile({ conn: api, filename });
         expect(api.addRecord).toHaveBeenCalled();

From 849fe4b705987ae12eb822b438694b27b036eec4 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:28:26 -0800
Subject: [PATCH 19/29] Remove node-expat library

---
 package-lock.json | 56 -----------------------------------------------
 package.json      |  1 -
 2 files changed, 57 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 100a44d4..58541d69 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -23,7 +23,6 @@
         "jsonpath": "^1.1.1",
         "jsonwebtoken": "^9.0.2",
         "lodash": "^4.17.21",
-        "node-expat": "^2.3.18",
         "node-fetch": "^2.6.7",
         "p-limit": "^3.1.0",
         "parse5": "^5.1.1",
@@ -2875,14 +2874,6 @@
         "node": "*"
       }
     },
-    "node_modules/bindings": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
-      "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
-      "dependencies": {
-        "file-uri-to-path": "1.0.0"
-      }
-    },
     "node_modules/bluebird": {
       "version": "3.4.7",
       "resolved": "https://registry.npmjs.org/bluebird/-/bluebird-3.4.7.tgz",
@@ -4814,11 +4805,6 @@
         "node": "^10.12.0 || >=12.0.0"
       }
     },
-    "node_modules/file-uri-to-path": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
-      "integrity": "sha512-0Zt+s3L7Vf1biwWZ29aARiVYLx7iMGnEUl9x33fbB/j3jR81u/O2LbqK+Bm1CDSNDKVtJ/YjwY7TUd5SkeLQLw=="
-    },
     "node_modules/fill-range": {
       "version": "7.1.1",
       "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
@@ -10138,27 +10124,12 @@
         "node": ">= 6"
       }
     },
-    "node_modules/nan": {
-      "version": "2.22.0",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.22.0.tgz",
-      "integrity": "sha512-nbajikzWTMwsW+eSsNm3QwlOs7het9gGJU5dDZzRTQGk03vyBOauxgI4VakDzE0PtsGTmXPsXTbbjVhRwR5mpw=="
-    },
     "node_modules/natural-compare": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/natural-compare/-/natural-compare-1.4.0.tgz",
       "integrity": "sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc=",
       "dev": true
     },
-    "node_modules/node-expat": {
-      "version": "2.3.18",
-      "resolved": "https://registry.npmjs.org/node-expat/-/node-expat-2.3.18.tgz",
-      "integrity": "sha512-9dIrDxXePa9HSn+hhlAg1wXkvqOjxefEbMclGxk2cEnq/Y3U7Qo5HNNqeo3fQ4bVmLhcdt3YN1TZy7WMZy4MHw==",
-      "hasInstallScript": true,
-      "dependencies": {
-        "bindings": "^1.5.0",
-        "nan": "^2.13.2"
-      }
-    },
     "node_modules/node-fetch": {
       "version": "2.6.7",
       "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
@@ -14208,14 +14179,6 @@
         "chainsaw": "~0.1.0"
       }
     },
-    "bindings": {
-      "version": "1.5.0",
-      "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
-      "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
-      "requires": {
-        "file-uri-to-path": "1.0.0"
-      }
-    },
     "bluebird": {
       "version": "3.4.7",
       "resolved": "https://registry.npmjs.org/bluebird/-/bluebird-3.4.7.tgz",
@@ -15688,11 +15651,6 @@
         "flat-cache": "^3.0.4"
       }
     },
-    "file-uri-to-path": {
-      "version": "1.0.0",
-      "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
-      "integrity": "sha512-0Zt+s3L7Vf1biwWZ29aARiVYLx7iMGnEUl9x33fbB/j3jR81u/O2LbqK+Bm1CDSNDKVtJ/YjwY7TUd5SkeLQLw=="
-    },
     "fill-range": {
       "version": "7.1.1",
       "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
@@ -19803,26 +19761,12 @@
         }
       }
     },
-    "nan": {
-      "version": "2.22.0",
-      "resolved": "https://registry.npmjs.org/nan/-/nan-2.22.0.tgz",
-      "integrity": "sha512-nbajikzWTMwsW+eSsNm3QwlOs7het9gGJU5dDZzRTQGk03vyBOauxgI4VakDzE0PtsGTmXPsXTbbjVhRwR5mpw=="
-    },
     "natural-compare": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/natural-compare/-/natural-compare-1.4.0.tgz",
       "integrity": "sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc=",
       "dev": true
     },
-    "node-expat": {
-      "version": "2.3.18",
-      "resolved": "https://registry.npmjs.org/node-expat/-/node-expat-2.3.18.tgz",
-      "integrity": "sha512-9dIrDxXePa9HSn+hhlAg1wXkvqOjxefEbMclGxk2cEnq/Y3U7Qo5HNNqeo3fQ4bVmLhcdt3YN1TZy7WMZy4MHw==",
-      "requires": {
-        "bindings": "^1.5.0",
-        "nan": "^2.13.2"
-      }
-    },
     "node-fetch": {
       "version": "2.6.7",
       "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
diff --git a/package.json b/package.json
index ec0a3ee2..2653c62b 100644
--- a/package.json
+++ b/package.json
@@ -26,7 +26,6 @@
     "jsonpath": "^1.1.1",
     "jsonwebtoken": "^9.0.2",
     "lodash": "^4.17.21",
-    "node-expat": "^2.3.18",
     "node-fetch": "^2.6.7",
     "p-limit": "^3.1.0",
     "parse5": "^5.1.1",

From 4098875367b90ab4da8ea5145fd0457018298572 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:33:04 -0800
Subject: [PATCH 20/29] upgrade jest

---
 package-lock.json | 529 ++++++++++++++++++++++++++++------------------
 package.json      |   2 +-
 2 files changed, 321 insertions(+), 210 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 58541d69..8fd6959a 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -33,7 +33,7 @@
         "xml2js": "^0.6.2"
       },
       "devDependencies": {
-        "eslint": "^8.17.0",
+        "eslint": "^8.44.0",
         "eslint-config-airbnb": "^19.0.4",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-jest": "^28.10.0",
@@ -675,22 +675,43 @@
         "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
       }
     },
+    "node_modules/@eslint-community/regexpp": {
+      "version": "4.12.1",
+      "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.12.1.tgz",
+      "integrity": "sha512-CCZCDJuduB9OUkFkY2IgppNZMi2lBQgD2qzwXkEia16cge2pijY/aXi96CJMquDMn3nJdlPV1A5KrJEXwfLNzQ==",
+      "dev": true,
+      "engines": {
+        "node": "^12.0.0 || ^14.0.0 || >=16.0.0"
+      }
+    },
     "node_modules/@eslint/eslintrc": {
-      "version": "1.3.0",
-      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-1.3.0.tgz",
-      "integrity": "sha512-UWW0TMTmk2d7hLcWD1/e2g5HDM/HQ3csaLSqXCfqwh4uNDuNqlaKWXmEsL4Cs41Z0KnILNvwbHAah3C2yt06kw==",
+      "version": "2.1.4",
+      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.1.4.tgz",
+      "integrity": "sha512-269Z39MS6wVJtsoUl10L60WdkhJVdPG24Q4eZTH3nnF6lpvSShEK3wQjDX9JRWAUPvPh7COouPpU9IrqaZFvtQ==",
       "dev": true,
       "dependencies": {
         "ajv": "^6.12.4",
         "debug": "^4.3.2",
-        "espree": "^9.3.2",
-        "globals": "^13.15.0",
+        "espree": "^9.6.0",
+        "globals": "^13.19.0",
         "ignore": "^5.2.0",
         "import-fresh": "^3.2.1",
         "js-yaml": "^4.1.0",
         "minimatch": "^3.1.2",
         "strip-json-comments": "^3.1.1"
       },
+      "engines": {
+        "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+      },
+      "funding": {
+        "url": "https://opencollective.com/eslint"
+      }
+    },
+    "node_modules/@eslint/js": {
+      "version": "8.57.1",
+      "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.57.1.tgz",
+      "integrity": "sha512-d9zaMRSTIKDLhctzH12MtXvJKSSUhaHcjV+2Z+GK+EEY7XKpP5yR4x+N3TAcHTcu963nIr+TMcCb4DBCYX1z6Q==",
+      "dev": true,
       "engines": {
         "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
       }
@@ -733,23 +754,38 @@
       "integrity": "sha512-j11XSuRuAlft6vLDEX4RvhqC0KxNxx6QIyMXNb0vHHSNPXTPeiy3algESWmOOIzEtiEL0qiowPU3ewW9hHVa7Q=="
     },
     "node_modules/@humanwhocodes/config-array": {
-      "version": "0.9.5",
-      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.9.5.tgz",
-      "integrity": "sha512-ObyMyWxZiCu/yTisA7uzx81s40xR2fD5Cg/2Kq7G02ajkNubJf6BopgDTmDyc3U7sXpNKM8cYOw7s7Tyr+DnCw==",
+      "version": "0.13.0",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.13.0.tgz",
+      "integrity": "sha512-DZLEEqFWQFiyK6h5YIeynKx7JlvCYWL0cImfSRXZ9l4Sg2efkFGTuFf6vzXjK1cq6IYkU+Eg/JizXw+TD2vRNw==",
+      "deprecated": "Use @eslint/config-array instead",
       "dev": true,
       "dependencies": {
-        "@humanwhocodes/object-schema": "^1.2.1",
-        "debug": "^4.1.1",
-        "minimatch": "^3.0.4"
+        "@humanwhocodes/object-schema": "^2.0.3",
+        "debug": "^4.3.1",
+        "minimatch": "^3.0.5"
       },
       "engines": {
         "node": ">=10.10.0"
       }
     },
+    "node_modules/@humanwhocodes/module-importer": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/module-importer/-/module-importer-1.0.1.tgz",
+      "integrity": "sha512-bxveV4V8v5Yb4ncFTT3rPSgZBOpCkjfK0y4oVVVJwIuDVBRMDXrPyXRL988i5ap9m9bnyEEjWfm5WkBmtffLfA==",
+      "dev": true,
+      "engines": {
+        "node": ">=12.22"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/nzakas"
+      }
+    },
     "node_modules/@humanwhocodes/object-schema": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-1.2.1.tgz",
-      "integrity": "sha512-ZnQMnLV4e7hDlUvw8H+U8ASL02SS2Gn6+9Ac3wGGLIe7+je2AeAOxPY+izIPJDfFDb7eDjev0Us8MO1iFRN8hA==",
+      "version": "2.0.3",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-2.0.3.tgz",
+      "integrity": "sha512-93zYdMES/c1D69yZiKDBj0V24vqNzB/koF26KPaagAfd3P/4gUlh3Dys5ogAK+Exi9QyzlD8x/08Zt7wIKcDcA==",
+      "deprecated": "Use @eslint/object-schema instead",
       "dev": true
     },
     "node_modules/@istanbuljs/load-nyc-config": {
@@ -2395,6 +2431,12 @@
         "url": "https://opencollective.com/eslint"
       }
     },
+    "node_modules/@ungap/structured-clone": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.1.tgz",
+      "integrity": "sha512-fEzPV3hSkSMltkw152tJKNARhOupqbH96MZWyRjNaYZOMIzbrTeQDG+MTc6Mr2pgzFQzFxAfmhGDNP5QK++2ZA==",
+      "dev": true
+    },
     "node_modules/@xmldom/xmldom": {
       "version": "0.8.6",
       "resolved": "https://registry.npmjs.org/@xmldom/xmldom/-/xmldom-0.8.6.tgz",
@@ -2421,9 +2463,9 @@
       }
     },
     "node_modules/acorn": {
-      "version": "8.7.1",
-      "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.7.1.tgz",
-      "integrity": "sha512-Xx54uLJQZ19lKygFXOWsscKUbsBZW0CPykPhVQdhIeIwrbPmJzqeASDInc8nKBnp/JT6igTs82qPXz069H8I/A==",
+      "version": "8.14.0",
+      "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.14.0.tgz",
+      "integrity": "sha512-cl669nCJTZBsL97OF4kUQm5g5hC2uihk0NxY3WENAC0TYdILVkAyHymAntgxGkl7K+t0cXIrH5siy5S4XkFycA==",
       "dev": true,
       "bin": {
         "acorn": "bin/acorn"
@@ -3712,46 +3754,50 @@
       }
     },
     "node_modules/eslint": {
-      "version": "8.17.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.17.0.tgz",
-      "integrity": "sha512-gq0m0BTJfci60Fz4nczYxNAlED+sMcihltndR8t9t1evnU/azx53x3t2UHXC/uRjcbvRw/XctpaNygSTcQD+Iw==",
-      "dev": true,
-      "dependencies": {
-        "@eslint/eslintrc": "^1.3.0",
-        "@humanwhocodes/config-array": "^0.9.2",
-        "ajv": "^6.10.0",
+      "version": "8.57.1",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.57.1.tgz",
+      "integrity": "sha512-ypowyDxpVSYpkXr9WPv2PAZCtNip1Mv5KTW0SCurXv/9iOpcrH9PaqUElksqEB6pChqHGDRCFTyrZlGhnLNGiA==",
+      "deprecated": "This version is no longer supported. Please see https://eslint.org/version-support for other options.",
+      "dev": true,
+      "dependencies": {
+        "@eslint-community/eslint-utils": "^4.2.0",
+        "@eslint-community/regexpp": "^4.6.1",
+        "@eslint/eslintrc": "^2.1.4",
+        "@eslint/js": "8.57.1",
+        "@humanwhocodes/config-array": "^0.13.0",
+        "@humanwhocodes/module-importer": "^1.0.1",
+        "@nodelib/fs.walk": "^1.2.8",
+        "@ungap/structured-clone": "^1.2.0",
+        "ajv": "^6.12.4",
         "chalk": "^4.0.0",
         "cross-spawn": "^7.0.2",
         "debug": "^4.3.2",
         "doctrine": "^3.0.0",
         "escape-string-regexp": "^4.0.0",
-        "eslint-scope": "^7.1.1",
-        "eslint-utils": "^3.0.0",
-        "eslint-visitor-keys": "^3.3.0",
-        "espree": "^9.3.2",
-        "esquery": "^1.4.0",
+        "eslint-scope": "^7.2.2",
+        "eslint-visitor-keys": "^3.4.3",
+        "espree": "^9.6.1",
+        "esquery": "^1.4.2",
         "esutils": "^2.0.2",
         "fast-deep-equal": "^3.1.3",
         "file-entry-cache": "^6.0.1",
-        "functional-red-black-tree": "^1.0.1",
-        "glob-parent": "^6.0.1",
-        "globals": "^13.15.0",
+        "find-up": "^5.0.0",
+        "glob-parent": "^6.0.2",
+        "globals": "^13.19.0",
+        "graphemer": "^1.4.0",
         "ignore": "^5.2.0",
-        "import-fresh": "^3.0.0",
         "imurmurhash": "^0.1.4",
         "is-glob": "^4.0.0",
+        "is-path-inside": "^3.0.3",
         "js-yaml": "^4.1.0",
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+      "version": "8.14.0",
+      "resolved": "https://registry.npmjs.org/acorn/-/acorn-8.14.0.tgz",
+      "integrity": "sha512-cl669nCJTZBsL97OF4kUQm5g5hC2uihk0NxY3WENAC0TYdILVkAyHymAntgxGkl7K+t0cXIrH5siy5S4XkFycA==",
       "dev": true
     },
     "acorn-globals": {
@@ -14859,46 +14954,49 @@
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     },
     "eslint": {
-      "version": "8.17.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.17.0.tgz",
-      "integrity": "sha512-gq0m0BTJfci60Fz4nczYxNAlED+sMcihltndR8t9t1evnU/azx53x3t2UHXC/uRjcbvRw/XctpaNygSTcQD+Iw==",
-      "dev": true,
-      "requires": {
-        "@eslint/eslintrc": "^1.3.0",
-        "@humanwhocodes/config-array": "^0.9.2",
-        "ajv": "^6.10.0",
+      "version": "8.57.1",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.57.1.tgz",
+      "integrity": "sha512-ypowyDxpVSYpkXr9WPv2PAZCtNip1Mv5KTW0SCurXv/9iOpcrH9PaqUElksqEB6pChqHGDRCFTyrZlGhnLNGiA==",
+      "dev": true,
+      "requires": {
+        "@eslint-community/eslint-utils": "^4.2.0",
+        "@eslint-community/regexpp": "^4.6.1",
+        "@eslint/eslintrc": "^2.1.4",
+        "@eslint/js": "8.57.1",
+        "@humanwhocodes/config-array": "^0.13.0",
+        "@humanwhocodes/module-importer": "^1.0.1",
+        "@nodelib/fs.walk": "^1.2.8",
+        "@ungap/structured-clone": "^1.2.0",
+        "ajv": "^6.12.4",
         "chalk": "^4.0.0",
         "cross-spawn": "^7.0.2",
         "debug": "^4.3.2",
         "doctrine": "^3.0.0",
         "escape-string-regexp": "^4.0.0",
-        "eslint-scope": "^7.1.1",
-        "eslint-utils": "^3.0.0",
-        "eslint-visitor-keys": "^3.3.0",
-        "espree": "^9.3.2",
-        "esquery": "^1.4.0",
+        "eslint-scope": "^7.2.2",
+        "eslint-visitor-keys": "^3.4.3",
+        "espree": "^9.6.1",
+        "esquery": "^1.4.2",
         "esutils": "^2.0.2",
         "fast-deep-equal": "^3.1.3",
         "file-entry-cache": "^6.0.1",
-        "functional-red-black-tree": "^1.0.1",
-        "glob-parent": "^6.0.1",
-        "globals": "^13.15.0",
+        "find-up": "^5.0.0",
+        "glob-parent": "^6.0.2",
+        "globals": "^13.19.0",
+        "graphemer": "^1.4.0",
         "ignore": "^5.2.0",
-        "import-fresh": "^3.0.0",
         "imurmurhash": "^0.1.4",
         "is-glob": "^4.0.0",
+        "is-path-inside": "^3.0.3",
         "js-yaml": "^4.1.0",
         "json-stable-stringify-without-jsonify": "^1.0.1",
         "levn": "^0.4.1",
         "lodash.merge": "^4.6.2",
         "minimatch": "^3.1.2",
         "natural-compare": "^1.4.0",
-        "optionator": "^0.9.1",
-        "regexpp": "^3.2.0",
+        "optionator": "^0.9.3",
         "strip-ansi": "^6.0.1",
-        "strip-json-comments": "^3.1.0",
-        "text-table": "^0.2.0",
-        "v8-compile-cache": "^2.0.3"
+        "text-table": "^0.2.0"
       },
       "dependencies": {
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@@ -14956,22 +15054,16 @@
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           "dev": true
         },
-        "eslint-scope": {
-          "version": "7.1.1",
-          "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.1.1.tgz",
-          "integrity": "sha512-QKQM/UXpIiHcLqJ5AOyIW7XZmzjkzQXYE54n1++wb0u9V/abW3l9uQnxX8Z5Xd18xyKIMTUAyQ0k1e8pz6LUrw==",
+        "find-up": {
+          "version": "5.0.0",
+          "resolved": "https://registry.npmjs.org/find-up/-/find-up-5.0.0.tgz",
+          "integrity": "sha512-78/PXT1wlLLDgTzDs7sjq9hzz0vXD+zn+7wypEe4fXQxCmdmqfGsEPQxmiCSQI3ajFV91bVSsvNtrJRiW6nGng==",
           "dev": true,
           "requires": {
-            "esrecurse": "^4.3.0",
-            "estraverse": "^5.2.0"
+            "locate-path": "^6.0.0",
+            "path-exists": "^4.0.0"
           }
         },
-        "estraverse": {
-          "version": "5.3.0",
-          "resolved": "https://registry.npmjs.org/estraverse/-/estraverse-5.3.0.tgz",
-          "integrity": "sha512-MMdARuVEQziNTeJD8DgMqmhwR11BRQ/cBP+pLtYdSTnf3MIO8fFeiINEbX36ZdNlfU/7A9f3gUw49B3oQsvwBA==",
-          "dev": true
-        },
         "has-flag": {
           "version": "4.0.0",
           "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
@@ -14988,10 +15080,19 @@
             "type-check": "~0.4.0"
           }
         },
+        "locate-path": {
+          "version": "6.0.0",
+          "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-6.0.0.tgz",
+          "integrity": "sha512-iPZK6eYjbxRu3uB4/WZ3EsEIMJFMqAoopl3R+zuq0UjcAm/MO6KCweDgPfP3elTztoKP3KtnVHxTn2NHBSDVUw==",
+          "dev": true,
+          "requires": {
+            "p-locate": "^5.0.0"
+          }
+        },
         "optionator": {
-          "version": "0.9.1",
-          "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.1.tgz",
-          "integrity": "sha512-74RlY5FCnhq4jRxVUPKDaRwrVNXMqsGsiW6AJw4XK8hmtm10wC0ypZBLw5IIp85NZMr91+qd1RvvENwg7jjRFw==",
+          "version": "0.9.4",
+          "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.4.tgz",
+          "integrity": "sha512-6IpQ7mKUxRcZNLIObR0hz7lxsapSSIYNZJwXPGeF0mTVqGKFIXj1DQcMoT22S3ROcLyY/rz0PWaWZ9ayWmad9g==",
           "dev": true,
           "requires": {
             "deep-is": "^0.1.3",
@@ -14999,9 +15100,24 @@
             "levn": "^0.4.1",
             "prelude-ls": "^1.2.1",
             "type-check": "^0.4.0",
-            "word-wrap": "^1.2.3"
+            "word-wrap": "^1.2.5"
+          }
+        },
+        "p-locate": {
+          "version": "5.0.0",
+          "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-5.0.0.tgz",
+          "integrity": "sha512-LaNjtRWUBY++zB5nE/NwcaoMylSPk+S+ZHNB1TzdbMJMny6dynpAGt7X/tl/QYq3TIeE6nxHppbo2LGymrG5Pw==",
+          "dev": true,
+          "requires": {
+            "p-limit": "^3.0.2"
           }
         },
+        "path-exists": {
+          "version": "4.0.0",
+          "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
+          "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==",
+          "dev": true
+        },
         "prelude-ls": {
           "version": "1.2.1",
           "resolved": "https://registry.npmjs.org/prelude-ls/-/prelude-ls-1.2.1.tgz",
@@ -15271,19 +15387,20 @@
         "requireindex": "~1.2.0"
       }
     },
-    "eslint-utils": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-3.0.0.tgz",
-      "integrity": "sha512-uuQC43IGctw68pJA1RgbQS8/NP7rch6Cwd4j3ZBtgo4/8Flj4eGE7ZYSZRN3iq5pVUv6GPdW5Z1RFleo84uLDA==",
+    "eslint-scope": {
+      "version": "7.2.2",
+      "resolved": "https://registry.npmjs.org/eslint-scope/-/eslint-scope-7.2.2.tgz",
+      "integrity": "sha512-dOt21O7lTMhDM+X9mB4GX+DZrZtCUJPL/wlcTqxyrx5IvO0IYtILdtrQGQp+8n5S0gwSVmOf9NQrjMOgfQZlIg==",
       "dev": true,
       "requires": {
-        "eslint-visitor-keys": "^2.0.0"
+        "esrecurse": "^4.3.0",
+        "estraverse": "^5.2.0"
       },
       "dependencies": {
-        "eslint-visitor-keys": {
-          "version": "2.1.0",
-          "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-2.1.0.tgz",
-          "integrity": "sha512-0rSmRBzXgDzIsD6mGdJgevzgezI534Cer5L/vyMX0kHzT/jiB43jRhd9YUlMGYLQy2zprNmoT8qasCGtY+QaKw==",
+        "estraverse": {
+          "version": "5.3.0",
+          "resolved": "https://registry.npmjs.org/estraverse/-/estraverse-5.3.0.tgz",
+          "integrity": "sha512-MMdARuVEQziNTeJD8DgMqmhwR11BRQ/cBP+pLtYdSTnf3MIO8fFeiINEbX36ZdNlfU/7A9f3gUw49B3oQsvwBA==",
           "dev": true
         }
       }
@@ -15300,14 +15417,14 @@
       "integrity": "sha512-U1suiZ2oDVWv4zPO56S0NcR5QriEahGtdN2OR6FiOG4WJvcjBVFB0qI4+eKoWFH483PKGuLuu6V8Z4T5g63UVA=="
     },
     "espree": {
-      "version": "9.3.2",
-      "resolved": "https://registry.npmjs.org/espree/-/espree-9.3.2.tgz",
-      "integrity": "sha512-D211tC7ZwouTIuY5x9XnS0E9sWNChB7IYKX/Xp5eQj3nFXhqmiUDB9q27y76oFl8jTg3pXcQx/bpxMfs3CIZbA==",
+      "version": "9.6.1",
+      "resolved": "https://registry.npmjs.org/espree/-/espree-9.6.1.tgz",
+      "integrity": "sha512-oruZaFkjorTpF32kDSI5/75ViwGeZginGGy2NoOSg3Q9bnwlnmDm4HLnkl0RE3n+njDXR037aY1+x58Z/zFdwQ==",
       "dev": true,
       "requires": {
-        "acorn": "^8.7.1",
+        "acorn": "^8.9.0",
         "acorn-jsx": "^5.3.2",
-        "eslint-visitor-keys": "^3.3.0"
+        "eslint-visitor-keys": "^3.4.1"
       }
     },
     "esprima": {
@@ -15316,9 +15433,9 @@
       "integrity": "sha1-dqD9Zvz+FU/SkmZ9wmQBl1CxZXs="
     },
     "esquery": {
-      "version": "1.4.0",
-      "resolved": "https://registry.npmjs.org/esquery/-/esquery-1.4.0.tgz",
-      "integrity": "sha512-cCDispWt5vHHtwMY2YrAQ4ibFkAL8RbH5YGBnZBc90MolvvfkkQcJro/aZiAQUlQ3qgrYS6D6v8Gc5G5CQsc9w==",
+      "version": "1.6.0",
+      "resolved": "https://registry.npmjs.org/esquery/-/esquery-1.6.0.tgz",
+      "integrity": "sha512-ca9pw9fomFcKPvFLXhBKUK90ZvGibiGOvRJNbjljY7s7uq/5YO4BOzcYtJqExdx99rF6aAcnRxHmcUHcz6sQsg==",
       "dev": true,
       "requires": {
         "estraverse": "^5.1.0"
@@ -15737,12 +15854,6 @@
         "functions-have-names": "^1.2.2"
       }
     },
-    "functional-red-black-tree": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/functional-red-black-tree/-/functional-red-black-tree-1.0.1.tgz",
-      "integrity": "sha1-GwqzvVU7Kg1jmdKcDj6gslIHgyc=",
-      "dev": true
-    },
     "functions-have-names": {
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/functions-have-names/-/functions-have-names-1.2.3.tgz",
@@ -15823,9 +15934,9 @@
       "dev": true
     },
     "globals": {
-      "version": "13.15.0",
-      "resolved": "https://registry.npmjs.org/globals/-/globals-13.15.0.tgz",
-      "integrity": "sha512-bpzcOlgDhMG070Av0Vy5Owklpv1I6+j96GhUI7Rh7IzDCKLzboflLrrfqMu8NquDbiR4EOQk7XzJwqVJxicxog==",
+      "version": "13.24.0",
+      "resolved": "https://registry.npmjs.org/globals/-/globals-13.24.0.tgz",
+      "integrity": "sha512-AhO5QUcj8llrbG09iWhPU2B204J1xnPeL8kQmVorSsy+Sjj1sk8gIyh6cUocGmH4L0UuhAJy+hJMRA4mgA4mFQ==",
       "dev": true,
       "requires": {
         "type-fest": "^0.20.2"
@@ -15836,6 +15947,12 @@
       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.10.tgz",
       "integrity": "sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA=="
     },
+    "graphemer": {
+      "version": "1.4.0",
+      "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
+      "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==",
+      "dev": true
+    },
     "has": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/has/-/has-1.0.3.tgz",
@@ -15996,9 +16113,9 @@
       }
     },
     "ignore": {
-      "version": "5.2.0",
-      "resolved": "https://registry.npmjs.org/ignore/-/ignore-5.2.0.tgz",
-      "integrity": "sha512-CmxgYGiEPCLhfLnpPp1MoRmifwEIOgjcHXxOBjv7mY96c+eWScsOP9c112ZyLdWHi0FxHjI+4uVhKYp/gcdRmQ==",
+      "version": "5.3.2",
+      "resolved": "https://registry.npmjs.org/ignore/-/ignore-5.3.2.tgz",
+      "integrity": "sha512-hsBTNUqQTDwkWtcdYI2i06Y/nUBEsNEDJKjWdigLvegy8kDuJAS8uRlpkkcQpyEXL0Z/pjDy5HBmMjRCJ2gq+g==",
       "dev": true
     },
     "immediate": {
@@ -16212,6 +16329,12 @@
         "has-tostringtag": "^1.0.0"
       }
     },
+    "is-path-inside": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/is-path-inside/-/is-path-inside-3.0.3.tgz",
+      "integrity": "sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ==",
+      "dev": true
+    },
     "is-potential-custom-element-name": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/is-potential-custom-element-name/-/is-potential-custom-element-name-1.0.1.tgz",
@@ -20185,12 +20308,6 @@
         "functions-have-names": "^1.2.2"
       }
     },
-    "regexpp": {
-      "version": "3.2.0",
-      "resolved": "https://registry.npmjs.org/regexpp/-/regexpp-3.2.0.tgz",
-      "integrity": "sha512-pq2bWo9mVD43nbts2wGv17XLiNLya+GklZ8kaDLV2Z08gDCsGpnKn9BFMepvWuHCbyVvY7J5o5+BVvoQbmlJLg==",
-      "dev": true
-    },
     "require-directory": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -20827,12 +20944,6 @@
       "resolved": "https://registry.npmjs.org/uuid-validate/-/uuid-validate-0.0.3.tgz",
       "integrity": "sha512-Fykw5U4eZESbq739BeLvEBFRuJODfrlmjx5eJux7W817LjRaq4b7/i4t2zxQmhcX+fAj4nMfRdTzO4tmwLKn0w=="
     },
-    "v8-compile-cache": {
-      "version": "2.3.0",
-      "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.3.0.tgz",
-      "integrity": "sha512-l8lCEmLcLYZh4nbunNZvQCJc5pv7+RCwa8q/LdUx8u7lsWvPDKmpodJAJNwkAhJC//dFY48KuIEmjtd4RViDrA==",
-      "dev": true
-    },
     "v8-to-istanbul": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-8.1.0.tgz",
diff --git a/package.json b/package.json
index 2653c62b..3ba1e3ed 100644
--- a/package.json
+++ b/package.json
@@ -36,7 +36,7 @@
     "xml2js": "^0.6.2"
   },
   "devDependencies": {
-    "eslint": "^8.17.0",
+    "eslint": "^8.44.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-jest": "^28.10.0",

From e2fc8e4060396e3d14e0a32fbad8d3606788ec54 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:43:17 -0800
Subject: [PATCH 21/29] Override @typescript-eslint/utils for
 eslint-plugin-jest

---
 package-lock.json | 5 ++---
 package.json      | 5 +++++
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 8fd6959a..b152c356 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -15270,12 +15270,11 @@
       "integrity": "sha512-hyMWUxkBH99HpXT3p8hc7REbEZK3D+nk8vHXGgpB+XXsi0gO4PxMSP+pjfUzb67GnV9yawV9a53eUmcde1CCZA==",
       "dev": true,
       "requires": {
-        "@typescript-eslint/utils": "^6.0.0 || ^7.0.0 || ^8.0.0"
+        "@typescript-eslint/utils": "^7.0.0"
       },
       "dependencies": {
         "@typescript-eslint/utils": {
-          "version": "8.19.0",
-          "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-8.19.0.tgz",
+          "version": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-8.19.0.tgz",
           "integrity": "sha512-PTBG+0oEMPH9jCZlfg07LCB2nYI0I317yyvXGfxnvGvw4SHIOuRnQ3kadyyXY6tGdChusIHIbM5zfIbp4M6tCg==",
           "dev": true,
           "requires": {
diff --git a/package.json b/package.json
index 3ba1e3ed..55bb5331 100644
--- a/package.json
+++ b/package.json
@@ -51,6 +51,11 @@
     "jest-circus": "^27.3.1",
     "jest-junit": "^13.0.0"
   },
+  "overrides": {
+    "eslint-plugin-jest": {
+      "@typescript-eslint/utils": "^7.0.0"
+    }
+  },
   "scripts": {
     "test": "NODE_ENV=test jest --config config/jest.config.js",
     "lint": "eslint -c .eslintrc.json src test",

From e60c4840cedca56acb6cb0e78d643aa2b6c9c99b Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:46:54 -0800
Subject: [PATCH 22/29] Revert upgrading jest

---
 package-lock.json | 2 +-
 package.json      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index b152c356..4ae78542 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -33,7 +33,7 @@
         "xml2js": "^0.6.2"
       },
       "devDependencies": {
-        "eslint": "^8.44.0",
+        "eslint": "^8.17.0",
         "eslint-config-airbnb": "^19.0.4",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-jest": "^28.10.0",
diff --git a/package.json b/package.json
index 55bb5331..fc9a51e8 100644
--- a/package.json
+++ b/package.json
@@ -36,7 +36,7 @@
     "xml2js": "^0.6.2"
   },
   "devDependencies": {
-    "eslint": "^8.44.0",
+    "eslint": "^8.17.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-jest": "^28.10.0",

From 0551d4a079896dca8fbe7789aeb4c41d5acd8000 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 14:50:37 -0800
Subject: [PATCH 23/29] remove auto-update on jest minor version

---
 package-lock.json | 684 +++++++++++++++++++++++-----------------------
 package.json      |   2 +-
 2 files changed, 343 insertions(+), 343 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 4ae78542..cdc67ce9 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -33,7 +33,7 @@
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       },
       "devDependencies": {
-        "eslint": "^8.17.0",
+        "eslint": "8.17.0",
         "eslint-config-airbnb": "^19.0.4",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-jest": "^28.10.0",
@@ -675,24 +675,15 @@
         "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
       }
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-    "node_modules/@eslint-community/regexpp": {
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-      "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.12.1.tgz",
-      "integrity": "sha512-CCZCDJuduB9OUkFkY2IgppNZMi2lBQgD2qzwXkEia16cge2pijY/aXi96CJMquDMn3nJdlPV1A5KrJEXwfLNzQ==",
-      "dev": true,
-      "engines": {
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-      }
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     "node_modules/@eslint/eslintrc": {
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-      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.1.4.tgz",
-      "integrity": "sha512-269Z39MS6wVJtsoUl10L60WdkhJVdPG24Q4eZTH3nnF6lpvSShEK3wQjDX9JRWAUPvPh7COouPpU9IrqaZFvtQ==",
+      "version": "1.4.1",
+      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-1.4.1.tgz",
+      "integrity": "sha512-XXrH9Uarn0stsyldqDYq8r++mROmWRI1xKMXa640Bb//SY1+ECYX6VzT6Lcx5frD0V30XieqJ0oX9I2Xj5aoMA==",
       "dev": true,
       "dependencies": {
         "ajv": "^6.12.4",
         "debug": "^4.3.2",
-        "espree": "^9.6.0",
+        "espree": "^9.4.0",
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         "ignore": "^5.2.0",
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@@ -707,15 +698,6 @@
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-    "node_modules/@eslint/js": {
-      "version": "8.57.1",
-      "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.57.1.tgz",
-      "integrity": "sha512-d9zaMRSTIKDLhctzH12MtXvJKSSUhaHcjV+2Z+GK+EEY7XKpP5yR4x+N3TAcHTcu963nIr+TMcCb4DBCYX1z6Q==",
-      "dev": true,
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@@ -754,37 +736,24 @@
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-      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.13.0.tgz",
-      "integrity": "sha512-DZLEEqFWQFiyK6h5YIeynKx7JlvCYWL0cImfSRXZ9l4Sg2efkFGTuFf6vzXjK1cq6IYkU+Eg/JizXw+TD2vRNw==",
+      "version": "0.9.5",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.9.5.tgz",
+      "integrity": "sha512-ObyMyWxZiCu/yTisA7uzx81s40xR2fD5Cg/2Kq7G02ajkNubJf6BopgDTmDyc3U7sXpNKM8cYOw7s7Tyr+DnCw==",
       "deprecated": "Use @eslint/config-array instead",
       "dev": true,
       "dependencies": {
-        "@humanwhocodes/object-schema": "^2.0.3",
-        "debug": "^4.3.1",
-        "minimatch": "^3.0.5"
+        "@humanwhocodes/object-schema": "^1.2.1",
+        "debug": "^4.1.1",
+        "minimatch": "^3.0.4"
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         "node": ">=10.10.0"
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-    "node_modules/@humanwhocodes/module-importer": {
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-      "resolved": "https://registry.npmjs.org/@humanwhocodes/module-importer/-/module-importer-1.0.1.tgz",
-      "integrity": "sha512-bxveV4V8v5Yb4ncFTT3rPSgZBOpCkjfK0y4oVVVJwIuDVBRMDXrPyXRL988i5ap9m9bnyEEjWfm5WkBmtffLfA==",
-      "dev": true,
-      "engines": {
-        "node": ">=12.22"
-      },
-      "funding": {
-        "type": "github",
-        "url": "https://github.com/sponsors/nzakas"
-      }
-    },
     "node_modules/@humanwhocodes/object-schema": {
-      "version": "2.0.3",
-      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-2.0.3.tgz",
-      "integrity": "sha512-93zYdMES/c1D69yZiKDBj0V24vqNzB/koF26KPaagAfd3P/4gUlh3Dys5ogAK+Exi9QyzlD8x/08Zt7wIKcDcA==",
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-1.2.1.tgz",
+      "integrity": "sha512-ZnQMnLV4e7hDlUvw8H+U8ASL02SS2Gn6+9Ac3wGGLIe7+je2AeAOxPY+izIPJDfFDb7eDjev0Us8MO1iFRN8hA==",
       "deprecated": "Use @eslint/object-schema instead",
       "dev": true
     },
@@ -2292,6 +2261,12 @@
         "@types/istanbul-lib-coverage": "*"
       }
     },
+    "node_modules/@types/json-schema": {
+      "version": "7.0.15",
+      "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.15.tgz",
+      "integrity": "sha512-5+fP8P8MFNC+AyZCDxrB2pkZFPGzqQWUzpSeuuVLvm8VMcorNYavBqoFcxK8bQz4Qsbn4oUEEem4wDLfcysGHA==",
+      "dev": true
+    },
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@@ -2310,6 +2285,12 @@
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       "dev": true
     },
+    "node_modules/@types/semver": {
+      "version": "7.5.8",
+      "resolved": "https://registry.npmjs.org/@types/semver/-/semver-7.5.8.tgz",
+      "integrity": "sha512-I8EUhyrgfLrcTkzV3TSsGyl1tSuPrEDzr0yd5m90UgNxQkyDXULk3b6MlQqTCpZpNtWe1K0hzclnZkTcLBe2UQ==",
+      "dev": true
+    },
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       "resolved": "https://registry.npmjs.org/@types/stack-utils/-/stack-utils-2.0.1.tgz",
@@ -2323,16 +2304,16 @@
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     },
     "node_modules/@typescript-eslint/scope-manager": {
-      "version": "8.19.0",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-8.19.0.tgz",
-      "integrity": "sha512-hkoJiKQS3GQ13TSMEiuNmSCvhz7ujyqD1x3ShbaETATHrck+9RaDdUbt+osXaUuns9OFwrDTTrjtwsU8gJyyRA==",
+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/scope-manager/-/scope-manager-7.2.0.tgz",
+      "integrity": "sha512-Qh976RbQM/fYtjx9hs4XkayYujB/aPwglw2choHmf3zBjB4qOywWSdt9+KLRdHubGcoSwBnXUH2sR3hkyaERRg==",
       "dev": true,
       "dependencies": {
-        "@typescript-eslint/types": "8.19.0",
-        "@typescript-eslint/visitor-keys": "8.19.0"
+        "@typescript-eslint/types": "7.2.0",
+        "@typescript-eslint/visitor-keys": "7.2.0"
       },
       "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+        "node": "^16.0.0 || >=18.0.0"
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@@ -2340,12 +2321,12 @@
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-      "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-8.19.0.tgz",
-      "integrity": "sha512-8XQ4Ss7G9WX8oaYvD4OOLCjIQYgRQxO+qCiR2V2s2GxI9AUpo7riNwo6jDhKtTcaJjT8PY54j2Yb33kWtSJsmA==",
+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/types/-/types-7.2.0.tgz",
+      "integrity": "sha512-XFtUHPI/abFhm4cbCDc5Ykc8npOKBSJePY3a3s+lwumt7XWJuzP5cZcfZ610MIPHjQjNsOLlYK8ASPaNG8UiyA==",
       "dev": true,
       "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+        "node": "^16.0.0 || >=18.0.0"
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@@ -2353,29 +2334,31 @@
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     },
     "node_modules/@typescript-eslint/typescript-estree": {
-      "version": "8.19.0",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-8.19.0.tgz",
-      "integrity": "sha512-WW9PpDaLIFW9LCbucMSdYUuGeFUz1OkWYS/5fwZwTA+l2RwlWFdJvReQqMUMBw4yJWJOfqd7An9uwut2Oj8sLw==",
+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/typescript-estree/-/typescript-estree-7.2.0.tgz",
+      "integrity": "sha512-cyxS5WQQCoBwSakpMrvMXuMDEbhOo9bNHHrNcEWis6XHx6KF518tkF1wBvKIn/tpq5ZpUYK7Bdklu8qY0MsFIA==",
       "dev": true,
       "dependencies": {
-        "@typescript-eslint/types": "8.19.0",
-        "@typescript-eslint/visitor-keys": "8.19.0",
+        "@typescript-eslint/types": "7.2.0",
+        "@typescript-eslint/visitor-keys": "7.2.0",
         "debug": "^4.3.4",
-        "fast-glob": "^3.3.2",
+        "globby": "^11.1.0",
         "is-glob": "^4.0.3",
-        "minimatch": "^9.0.4",
-        "semver": "^7.6.0",
-        "ts-api-utils": "^1.3.0"
+        "minimatch": "9.0.3",
+        "semver": "^7.5.4",
+        "ts-api-utils": "^1.0.1"
       },
       "engines": {
-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+        "node": "^16.0.0 || >=18.0.0"
       },
       "funding": {
         "type": "opencollective",
         "url": "https://opencollective.com/typescript-eslint"
       },
-      "peerDependencies": {
-        "typescript": ">=4.8.4 <5.8.0"
+      "peerDependenciesMeta": {
+        "typescript": {
+          "optional": true
+        }
       }
     },
     "node_modules/@typescript-eslint/typescript-estree/node_modules/brace-expansion": {
@@ -2388,9 +2371,9 @@
       }
     },
     "node_modules/@typescript-eslint/typescript-estree/node_modules/minimatch": {
-      "version": "9.0.5",
-      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.5.tgz",
-      "integrity": "sha512-G6T0ZX48xgozx7587koeX9Ys2NYy6Gmv//P89sEte9V9whIapMNF4idKxnW2QtCcLiTWlb/wfCabAtAFWhhBow==",
+      "version": "9.0.3",
+      "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-9.0.3.tgz",
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@@ -2403,40 +2386,22 @@
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+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-7.2.0.tgz",
+      "integrity": "sha512-c6EIQRHhcpl6+tO8EMR+kjkkV+ugUNXOmeASA1rlzkd8EPIriavpWoiEz1HR/VLhbVIdhqnV6E7JZm00cBDx2A==",
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-        "@typescript-eslint/types": "8.19.0",
-        "eslint-visitor-keys": "^4.2.0"
+        "@typescript-eslint/types": "7.2.0",
+        "eslint-visitor-keys": "^3.4.1"
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-        "node": "^18.18.0 || ^20.9.0 || >=21.1.0"
+        "node": "^16.0.0 || >=18.0.0"
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         "url": "https://opencollective.com/typescript-eslint"
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-      "funding": {
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-    "node_modules/@ungap/structured-clone": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.1.tgz",
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@@ -2603,6 +2568,15 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
+    "node_modules/array-union": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/array-union/-/array-union-2.1.0.tgz",
+      "integrity": "sha512-HGyxoOTYUyCM6stUe6EJgnd4EoewAI7zMdfqO+kGjnlZmBDz/cR5pf8r/cR4Wq60sL/p0IkcjUEEPwS3GFrIyw==",
+      "dev": true,
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/array.prototype.flat": {
       "version": "1.2.5",
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@@ -3512,6 +3486,18 @@
         "node": "^10.13.0 || ^12.13.0 || ^14.15.0 || >=15.0.0"
       }
     },
+    "node_modules/dir-glob": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/dir-glob/-/dir-glob-3.0.1.tgz",
+      "integrity": "sha512-WkrWp9GR4KXfKGYzOLmTuGVi1UWFfws377n9cc55/tb6DuqyF6pcQ5AbiHEshaDpY9v6oaSr2XCDidGmMwdzIA==",
+      "dev": true,
+      "dependencies": {
+        "path-type": "^4.0.0"
+      },
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/doctrine": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/doctrine/-/doctrine-2.1.0.tgz",
@@ -3754,50 +3740,47 @@
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-      "integrity": "sha512-ypowyDxpVSYpkXr9WPv2PAZCtNip1Mv5KTW0SCurXv/9iOpcrH9PaqUElksqEB6pChqHGDRCFTyrZlGhnLNGiA==",
+      "version": "8.17.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.17.0.tgz",
+      "integrity": "sha512-gq0m0BTJfci60Fz4nczYxNAlED+sMcihltndR8t9t1evnU/azx53x3t2UHXC/uRjcbvRw/XctpaNygSTcQD+Iw==",
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-        "@nodelib/fs.walk": "^1.2.8",
-        "@ungap/structured-clone": "^1.2.0",
-        "ajv": "^6.12.4",
+        "@eslint/eslintrc": "^1.3.0",
+        "@humanwhocodes/config-array": "^0.9.2",
+        "ajv": "^6.10.0",
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         "debug": "^4.3.2",
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-        "eslint-visitor-keys": "^3.4.3",
-        "espree": "^9.6.1",
-        "esquery": "^1.4.2",
+        "eslint-scope": "^7.1.1",
+        "eslint-utils": "^3.0.0",
+        "eslint-visitor-keys": "^3.3.0",
+        "espree": "^9.3.2",
+        "esquery": "^1.4.0",
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-        "glob-parent": "^6.0.2",
-        "globals": "^13.19.0",
-        "graphemer": "^1.4.0",
+        "functional-red-black-tree": "^1.0.1",
+        "glob-parent": "^6.0.1",
+        "globals": "^13.15.0",
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+        "import-fresh": "^3.0.0",
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-        "is-path-inside": "^3.0.3",
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         "minimatch": "^3.1.2",
         "natural-compare": "^1.4.0",
-        "optionator": "^0.9.3",
+        "optionator": "^0.9.1",
+        "regexpp": "^3.2.0",
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-        "text-table": "^0.2.0"
+        "strip-json-comments": "^3.1.0",
+        "text-table": "^0.2.0",
+        "v8-compile-cache": "^2.0.3"
       },
       "bin": {
         "eslint": "bin/eslint.js"
@@ -3979,26 +3962,28 @@
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+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-7.2.0.tgz",
+      "integrity": "sha512-YfHpnMAGb1Eekpm3XRK8hcMwGLGsnT6L+7b2XyRv6ouDuJU1tZir1GS2i0+VXRatMwSI1/UfcyPe53ADkU+IuA==",
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-        "@typescript-eslint/types": "8.19.0",
-        "@typescript-eslint/typescript-estree": "8.19.0"
+        "@types/json-schema": "^7.0.12",
+        "@types/semver": "^7.5.0",
+        "@typescript-eslint/scope-manager": "7.2.0",
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+          "integrity": "sha512-RHiac9mvaRw0x3AYRgDC1CxAP7HTcNrrECeA8YYJeWnpo+2Q5CegtZjaotWTWxDG3UeGA1coE05iH1mPjT/2mg==",
           "dev": true,
           "requires": {
             "brace-expansion": "^2.0.1"
@@ -13883,29 +13872,15 @@
       }
     },
     "@typescript-eslint/visitor-keys": {
-      "version": "8.19.0",
-      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-8.19.0.tgz",
-      "integrity": "sha512-mCFtBbFBJDCNCWUl5y6sZSCHXw1DEFEk3c/M3nRK2a4XUB8StGFtmcEMizdjKuBzB6e/smJAAWYug3VrdLMr1w==",
+      "version": "7.2.0",
+      "resolved": "https://registry.npmjs.org/@typescript-eslint/visitor-keys/-/visitor-keys-7.2.0.tgz",
+      "integrity": "sha512-c6EIQRHhcpl6+tO8EMR+kjkkV+ugUNXOmeASA1rlzkd8EPIriavpWoiEz1HR/VLhbVIdhqnV6E7JZm00cBDx2A==",
       "dev": true,
       "requires": {
-        "@typescript-eslint/types": "8.19.0",
-        "eslint-visitor-keys": "^4.2.0"
-      },
-      "dependencies": {
-        "eslint-visitor-keys": {
-          "version": "4.2.0",
-          "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-4.2.0.tgz",
-          "integrity": "sha512-UyLnSehNt62FFhSwjZlHmeokpRK59rcz29j+F1/aDgbkbRTk7wIc9XzdoasMUbRNKDM0qQt/+BJ4BrpFeABemw==",
-          "dev": true
-        }
+        "@typescript-eslint/types": "7.2.0",
+        "eslint-visitor-keys": "^3.4.1"
       }
     },
-    "@ungap/structured-clone": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.1.tgz",
-      "integrity": "sha512-fEzPV3hSkSMltkw152tJKNARhOupqbH96MZWyRjNaYZOMIzbrTeQDG+MTc6Mr2pgzFQzFxAfmhGDNP5QK++2ZA==",
-      "dev": true
-    },
     "@xmldom/xmldom": {
       "version": "0.8.6",
       "resolved": "https://registry.npmjs.org/@xmldom/xmldom/-/xmldom-0.8.6.tgz",
@@ -14029,6 +14004,12 @@
         "is-string": "^1.0.7"
       }
     },
+    "array-union": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/array-union/-/array-union-2.1.0.tgz",
+      "integrity": "sha512-HGyxoOTYUyCM6stUe6EJgnd4EoewAI7zMdfqO+kGjnlZmBDz/cR5pf8r/cR4Wq60sL/p0IkcjUEEPwS3GFrIyw==",
+      "dev": true
+    },
     "array.prototype.flat": {
       "version": "1.2.5",
       "resolved": "https://registry.npmjs.org/array.prototype.flat/-/array.prototype.flat-1.2.5.tgz",
@@ -14755,6 +14736,15 @@
       "integrity": "sha512-ag6wfpBFyNXZ0p8pcuIDS//D8H062ZQJ3fzYxjpmeKjnz8W4pekL3AI8VohmyZmsWW2PWaHgjsmqR6L13101VQ==",
       "dev": true
     },
+    "dir-glob": {
+      "version": "3.0.1",
+      "resolved": "https://registry.npmjs.org/dir-glob/-/dir-glob-3.0.1.tgz",
+      "integrity": "sha512-WkrWp9GR4KXfKGYzOLmTuGVi1UWFfws377n9cc55/tb6DuqyF6pcQ5AbiHEshaDpY9v6oaSr2XCDidGmMwdzIA==",
+      "dev": true,
+      "requires": {
+        "path-type": "^4.0.0"
+      }
+    },
     "doctrine": {
       "version": "2.1.0",
       "resolved": "https://registry.npmjs.org/doctrine/-/doctrine-2.1.0.tgz",
@@ -14954,49 +14944,46 @@
       }
     },
     "eslint": {
-      "version": "8.57.1",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.57.1.tgz",
-      "integrity": "sha512-ypowyDxpVSYpkXr9WPv2PAZCtNip1Mv5KTW0SCurXv/9iOpcrH9PaqUElksqEB6pChqHGDRCFTyrZlGhnLNGiA==",
-      "dev": true,
-      "requires": {
-        "@eslint-community/eslint-utils": "^4.2.0",
-        "@eslint-community/regexpp": "^4.6.1",
-        "@eslint/eslintrc": "^2.1.4",
-        "@eslint/js": "8.57.1",
-        "@humanwhocodes/config-array": "^0.13.0",
-        "@humanwhocodes/module-importer": "^1.0.1",
-        "@nodelib/fs.walk": "^1.2.8",
-        "@ungap/structured-clone": "^1.2.0",
-        "ajv": "^6.12.4",
+      "version": "8.17.0",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.17.0.tgz",
+      "integrity": "sha512-gq0m0BTJfci60Fz4nczYxNAlED+sMcihltndR8t9t1evnU/azx53x3t2UHXC/uRjcbvRw/XctpaNygSTcQD+Iw==",
+      "dev": true,
+      "requires": {
+        "@eslint/eslintrc": "^1.3.0",
+        "@humanwhocodes/config-array": "^0.9.2",
+        "ajv": "^6.10.0",
         "chalk": "^4.0.0",
         "cross-spawn": "^7.0.2",
         "debug": "^4.3.2",
         "doctrine": "^3.0.0",
         "escape-string-regexp": "^4.0.0",
-        "eslint-scope": "^7.2.2",
-        "eslint-visitor-keys": "^3.4.3",
-        "espree": "^9.6.1",
-        "esquery": "^1.4.2",
+        "eslint-scope": "^7.1.1",
+        "eslint-utils": "^3.0.0",
+        "eslint-visitor-keys": "^3.3.0",
+        "espree": "^9.3.2",
+        "esquery": "^1.4.0",
         "esutils": "^2.0.2",
         "fast-deep-equal": "^3.1.3",
         "file-entry-cache": "^6.0.1",
-        "find-up": "^5.0.0",
-        "glob-parent": "^6.0.2",
-        "globals": "^13.19.0",
-        "graphemer": "^1.4.0",
+        "functional-red-black-tree": "^1.0.1",
+        "glob-parent": "^6.0.1",
+        "globals": "^13.15.0",
         "ignore": "^5.2.0",
+        "import-fresh": "^3.0.0",
         "imurmurhash": "^0.1.4",
         "is-glob": "^4.0.0",
-        "is-path-inside": "^3.0.3",
         "js-yaml": "^4.1.0",
         "json-stable-stringify-without-jsonify": "^1.0.1",
         "levn": "^0.4.1",
         "lodash.merge": "^4.6.2",
         "minimatch": "^3.1.2",
         "natural-compare": "^1.4.0",
-        "optionator": "^0.9.3",
+        "optionator": "^0.9.1",
+        "regexpp": "^3.2.0",
         "strip-ansi": "^6.0.1",
-        "text-table": "^0.2.0"
+        "strip-json-comments": "^3.1.0",
+        "text-table": "^0.2.0",
+        "v8-compile-cache": "^2.0.3"
       },
       "dependencies": {
         "ansi-regex": {
@@ -15054,16 +15041,6 @@
           "integrity": "sha512-TtpcNJ3XAzx3Gq8sWRzJaVajRs0uVxA2YAkdb1jm2YkPz4G6egUFAyA3n5vtEIZefPk5Wa4UXbKuS5fKkJWdgA==",
           "dev": true
         },
-        "find-up": {
-          "version": "5.0.0",
-          "resolved": "https://registry.npmjs.org/find-up/-/find-up-5.0.0.tgz",
-          "integrity": "sha512-78/PXT1wlLLDgTzDs7sjq9hzz0vXD+zn+7wypEe4fXQxCmdmqfGsEPQxmiCSQI3ajFV91bVSsvNtrJRiW6nGng==",
-          "dev": true,
-          "requires": {
-            "locate-path": "^6.0.0",
-            "path-exists": "^4.0.0"
-          }
-        },
         "has-flag": {
           "version": "4.0.0",
           "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
@@ -15080,15 +15057,6 @@
             "type-check": "~0.4.0"
           }
         },
-        "locate-path": {
-          "version": "6.0.0",
-          "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-6.0.0.tgz",
-          "integrity": "sha512-iPZK6eYjbxRu3uB4/WZ3EsEIMJFMqAoopl3R+zuq0UjcAm/MO6KCweDgPfP3elTztoKP3KtnVHxTn2NHBSDVUw==",
-          "dev": true,
-          "requires": {
-            "p-locate": "^5.0.0"
-          }
-        },
         "optionator": {
           "version": "0.9.4",
           "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.4.tgz",
@@ -15103,21 +15071,6 @@
             "word-wrap": "^1.2.5"
           }
         },
-        "p-locate": {
-          "version": "5.0.0",
-          "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-5.0.0.tgz",
-          "integrity": "sha512-LaNjtRWUBY++zB5nE/NwcaoMylSPk+S+ZHNB1TzdbMJMny6dynpAGt7X/tl/QYq3TIeE6nxHppbo2LGymrG5Pw==",
-          "dev": true,
-          "requires": {
-            "p-limit": "^3.0.2"
-          }
-        },
-        "path-exists": {
-          "version": "4.0.0",
-          "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
-          "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==",
-          "dev": true
-        },
         "prelude-ls": {
           "version": "1.2.1",
           "resolved": "https://registry.npmjs.org/prelude-ls/-/prelude-ls-1.2.1.tgz",
@@ -15274,14 +15227,18 @@
       },
       "dependencies": {
         "@typescript-eslint/utils": {
-          "version": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-8.19.0.tgz",
-          "integrity": "sha512-PTBG+0oEMPH9jCZlfg07LCB2nYI0I317yyvXGfxnvGvw4SHIOuRnQ3kadyyXY6tGdChusIHIbM5zfIbp4M6tCg==",
+          "version": "7.2.0",
+          "resolved": "https://registry.npmjs.org/@typescript-eslint/utils/-/utils-7.2.0.tgz",
+          "integrity": "sha512-YfHpnMAGb1Eekpm3XRK8hcMwGLGsnT6L+7b2XyRv6ouDuJU1tZir1GS2i0+VXRatMwSI1/UfcyPe53ADkU+IuA==",
           "dev": true,
           "requires": {
             "@eslint-community/eslint-utils": "^4.4.0",
-            "@typescript-eslint/scope-manager": "8.19.0",
-            "@typescript-eslint/types": "8.19.0",
-            "@typescript-eslint/typescript-estree": "8.19.0"
+            "@types/json-schema": "^7.0.12",
+            "@types/semver": "^7.5.0",
+            "@typescript-eslint/scope-manager": "7.2.0",
+            "@typescript-eslint/types": "7.2.0",
+            "@typescript-eslint/typescript-estree": "7.2.0",
+            "semver": "^7.5.4"
           }
         }
       }
@@ -15404,6 +15361,23 @@
         }
       }
     },
+    "eslint-utils": {
+      "version": "3.0.0",
+      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-3.0.0.tgz",
+      "integrity": "sha512-uuQC43IGctw68pJA1RgbQS8/NP7rch6Cwd4j3ZBtgo4/8Flj4eGE7ZYSZRN3iq5pVUv6GPdW5Z1RFleo84uLDA==",
+      "dev": true,
+      "requires": {
+        "eslint-visitor-keys": "^2.0.0"
+      },
+      "dependencies": {
+        "eslint-visitor-keys": {
+          "version": "2.1.0",
+          "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-2.1.0.tgz",
+          "integrity": "sha512-0rSmRBzXgDzIsD6mGdJgevzgezI534Cer5L/vyMX0kHzT/jiB43jRhd9YUlMGYLQy2zprNmoT8qasCGtY+QaKw==",
+          "dev": true
+        }
+      }
+    },
     "eslint-visitor-keys": {
       "version": "3.4.3",
       "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz",
@@ -15853,6 +15827,12 @@
         "functions-have-names": "^1.2.2"
       }
     },
+    "functional-red-black-tree": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/functional-red-black-tree/-/functional-red-black-tree-1.0.1.tgz",
+      "integrity": "sha512-dsKNQNdj6xA3T+QlADDA7mOSlX0qiMINjn0cgr+eGHGsbSHzTabcIogz2+p/iqP1Xs6EP/sS2SbqH+brGTbq0g==",
+      "dev": true
+    },
     "functions-have-names": {
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/functions-have-names/-/functions-have-names-1.2.3.tgz",
@@ -15941,17 +15921,25 @@
         "type-fest": "^0.20.2"
       }
     },
+    "globby": {
+      "version": "11.1.0",
+      "resolved": "https://registry.npmjs.org/globby/-/globby-11.1.0.tgz",
+      "integrity": "sha512-jhIXaOzy1sb8IyocaruWSn1TjmnBVs8Ayhcy83rmxNJ8q2uWKCAj3CnJY+KpGSXCueAPc0i05kVvVKtP1t9S3g==",
+      "dev": true,
+      "requires": {
+        "array-union": "^2.1.0",
+        "dir-glob": "^3.0.1",
+        "fast-glob": "^3.2.9",
+        "ignore": "^5.2.0",
+        "merge2": "^1.4.1",
+        "slash": "^3.0.0"
+      }
+    },
     "graceful-fs": {
       "version": "4.2.10",
       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.10.tgz",
       "integrity": "sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA=="
     },
-    "graphemer": {
-      "version": "1.4.0",
-      "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
-      "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==",
-      "dev": true
-    },
     "has": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/has/-/has-1.0.3.tgz",
@@ -16328,12 +16316,6 @@
         "has-tostringtag": "^1.0.0"
       }
     },
-    "is-path-inside": {
-      "version": "3.0.3",
-      "resolved": "https://registry.npmjs.org/is-path-inside/-/is-path-inside-3.0.3.tgz",
-      "integrity": "sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ==",
-      "dev": true
-    },
     "is-potential-custom-element-name": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/is-potential-custom-element-name/-/is-potential-custom-element-name-1.0.1.tgz",
@@ -20146,6 +20128,12 @@
       "integrity": "sha512-G6zHoVqC6GGTQkZwF4lkuEyMbVOjoBKAEybQUypI1WTkqinCOrq2x6U2+phkJ1XsEMTy4LjtwPI7HW+NVrRR2w==",
       "dev": true
     },
+    "path-type": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/path-type/-/path-type-4.0.0.tgz",
+      "integrity": "sha512-gDKb8aZMDeD/tZWs9P6+q0J9Mwkdl6xMV8TjnGP3qJVJ06bdMgkbBlLU8IdfOsIsFz2BW1rNVT3XuNEl8zPAvw==",
+      "dev": true
+    },
     "picocolors": {
       "version": "1.0.0",
       "resolved": "https://registry.npmjs.org/picocolors/-/picocolors-1.0.0.tgz",
@@ -20307,6 +20295,12 @@
         "functions-have-names": "^1.2.2"
       }
     },
+    "regexpp": {
+      "version": "3.2.0",
+      "resolved": "https://registry.npmjs.org/regexpp/-/regexpp-3.2.0.tgz",
+      "integrity": "sha512-pq2bWo9mVD43nbts2wGv17XLiNLya+GklZ8kaDLV2Z08gDCsGpnKn9BFMepvWuHCbyVvY7J5o5+BVvoQbmlJLg==",
+      "dev": true
+    },
     "require-directory": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -20943,6 +20937,12 @@
       "resolved": "https://registry.npmjs.org/uuid-validate/-/uuid-validate-0.0.3.tgz",
       "integrity": "sha512-Fykw5U4eZESbq739BeLvEBFRuJODfrlmjx5eJux7W817LjRaq4b7/i4t2zxQmhcX+fAj4nMfRdTzO4tmwLKn0w=="
     },
+    "v8-compile-cache": {
+      "version": "2.4.0",
+      "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.4.0.tgz",
+      "integrity": "sha512-ocyWc3bAHBB/guyqJQVI5o4BZkPhznPYUG2ea80Gond/BgNWpap8TOmLSeeQG7bnh2KMISxskdADG59j7zruhw==",
+      "dev": true
+    },
     "v8-to-istanbul": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-8.1.0.tgz",
diff --git a/package.json b/package.json
index fc9a51e8..10ad395b 100644
--- a/package.json
+++ b/package.json
@@ -36,7 +36,7 @@
     "xml2js": "^0.6.2"
   },
   "devDependencies": {
-    "eslint": "^8.17.0",
+    "eslint": "8.17.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-jest": "^28.10.0",

From 0d9c5f148a22368f6e102a2a6035c32f4f05779e Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 15:00:27 -0800
Subject: [PATCH 24/29] Removing GH workflows/npm-test for v12 & v14

---
 .github/workflows/npm-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/npm-test.yml b/.github/workflows/npm-test.yml
index a37d3efb..e8ea4c46 100644
--- a/.github/workflows/npm-test.yml
+++ b/.github/workflows/npm-test.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: ['12', '14', '16']
+        node: ['16']
     name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2

From 5f2dd008609531ee0c42b4a9e03c0f0f2b47c054 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 15:05:55 -0800
Subject: [PATCH 25/29] drugbank temp fix

---
 src/drugbank/index.js | 115 +++++++++++++++++++++---------------------
 1 file changed, 58 insertions(+), 57 deletions(-)

diff --git a/src/drugbank/index.js b/src/drugbank/index.js
index 7ce2d007..877b8e94 100644
--- a/src/drugbank/index.js
+++ b/src/drugbank/index.js
@@ -276,63 +276,64 @@ const uploadFile = async ({ filename, conn, maxRecords }) => {
     await _chembl.preLoadCache(conn);
     const counts = { error: 0, skipped: 0, success: 0 };
 
-    // const parseXML = new Promise((resolve, reject) => {
-    //     logger.log('info', `loading XML data from ${filename}`);
-    //     const stream = fs.createReadStream(filename);
-    //     const xml = new XmlStream(stream);
-    //     xml.collect('drug drugbank-id');
-    //     xml.collect('drug external-identifier');
-    //     xml.collect('drug synonym');
-    //     xml.collect('drug categories > category');
-    //     xml.collect('drug atc-code level');
-    //     xml.collect('drug target polypeptide');
-    //     xml.collect('drug target actions action');
-    //     xml.collect('drug products product');
-    //     xml.collect('drug calculated-properties property');
-    //     xml.on('endElement: drug', (item) => {
-    //         if (Object.keys(item).length < 3) {
-    //             return;
-    //         }
-    //         xml.pause();
-    //         processRecord({
-    //             ATC, conn, drug: item, sources: { current: source, fda: fdaSource },
-    //         }).then(() => {
-    //             counts.success++;
-
-    //             if (maxRecords && (counts.success + counts.error + counts.skipped) >= maxRecords) {
-    //                 logger.warn(`not loading all content due to max records limit (${maxRecords})`);
-    //                 logger.info('Parsing stream complete');
-    //                 stream.close();
-    //                 resolve();
-    //             }
-
-    //             xml.resume();
-    //         }).catch((err) => {
-    //             let label;
-
-    //             try {
-    //                 label = getDrugBankId(item);
-    //             } catch (err2) {}  // eslint-disable-line
-    //             counts.error++;
-    //             logger.error(err);
-    //             logger.error(`Unable to process record ${label}`);
-    //             xml.resume();
-    //         });
-    //     });
-    //     xml.on('end', () => {
-    //         logger.info('Parsing stream complete');
-    //         stream.close();
-    //         resolve();
-    //     });
-    //     xml.on('error', (err) => {
-    //         logger.error('Parsing stream error');
-    //         logger.error(err);
-    //         stream.close();
-    //         reject(err);
-    //     });
-    // });
-
-    // await parseXML;
+    const parseXML = new Promise((resolve, reject) => {
+        logger.log('info', `loading XML data from ${filename}`);
+        const stream = fs.createReadStream(filename);
+        // const xml = new XmlStream(stream);
+        const xml = {};
+        xml.collect('drug drugbank-id');
+        xml.collect('drug external-identifier');
+        xml.collect('drug synonym');
+        xml.collect('drug categories > category');
+        xml.collect('drug atc-code level');
+        xml.collect('drug target polypeptide');
+        xml.collect('drug target actions action');
+        xml.collect('drug products product');
+        xml.collect('drug calculated-properties property');
+        xml.on('endElement: drug', (item) => {
+            if (Object.keys(item).length < 3) {
+                return;
+            }
+            xml.pause();
+            processRecord({
+                ATC, conn, drug: item, sources: { current: source, fda: fdaSource },
+            }).then(() => {
+                counts.success++;
+
+                if (maxRecords && (counts.success + counts.error + counts.skipped) >= maxRecords) {
+                    logger.warn(`not loading all content due to max records limit (${maxRecords})`);
+                    logger.info('Parsing stream complete');
+                    stream.close();
+                    resolve();
+                }
+
+                xml.resume();
+            }).catch((err) => {
+                let label;
+
+                try {
+                    label = getDrugBankId(item);
+                } catch (err2) {}  // eslint-disable-line
+                counts.error++;
+                logger.error(err);
+                logger.error(`Unable to process record ${label}`);
+                xml.resume();
+            });
+        });
+        xml.on('end', () => {
+            logger.info('Parsing stream complete');
+            stream.close();
+            resolve();
+        });
+        xml.on('error', (err) => {
+            logger.error('Parsing stream error');
+            logger.error(err);
+            stream.close();
+            reject(err);
+        });
+    });
+
+    await parseXML;
     logger.log('info', JSON.stringify(counts));
 };
 

From 25c98ddc37f9b7ac6dd2bda101a973ad1ca80cb8 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 15:08:23 -0800
Subject: [PATCH 26/29] disabling a civic test

---
 test/civic/civic.profile.test.js | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/test/civic/civic.profile.test.js b/test/civic/civic.profile.test.js
index ee8ea60d..752df4dc 100644
--- a/test/civic/civic.profile.test.js
+++ b/test/civic/civic.profile.test.js
@@ -226,16 +226,16 @@ describe('MolecularProfile.process()', () => {
         );
     });
 
-    test('test case that should throw a NotImplementedError', () => {
-        const molecularProfile = {
-            id: 1,
-            parsedName: [
-                { __typename: 'Feature' }, { id: 1 }, { text: 'AND' }, { text: 'NOT' }, { text: '(' },
-                { __typename: 'Feature' }, { id: 2 }, { text: 'OR' }, { __typename: 'Feature' }, { id: 3 }, { text: ')' },
-            ],
-        };
-        expect(() => MolecularProfile(molecularProfile).process()).toThrow(
-            `unable to process molecular profile with NOT operator (${molecularProfile.id || ''})`,
-        );
-    });
+    // test('test case that should throw a NotImplementedError', () => {
+    //     const molecularProfile = {
+    //         id: 1,
+    //         parsedName: [
+    //             { __typename: 'Feature' }, { id: 1 }, { text: 'AND' }, { text: 'NOT' }, { text: '(' },
+    //             { __typename: 'Feature' }, { id: 2 }, { text: 'OR' }, { __typename: 'Feature' }, { id: 3 }, { text: ')' },
+    //         ],
+    //     };
+    //     expect(() => MolecularProfile(molecularProfile).process()).toThrow(
+    //         `unable to process molecular profile with NOT operator (${molecularProfile.id || ''})`,
+    //     );
+    // });
 });

From bc1b918c389529369013a40c8261bc5c2df54d3e Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Fri, 3 Jan 2025 15:14:36 -0800
Subject: [PATCH 27/29] GH workflows/npm-test from  v12-14-16 to v16-18-20

---
 .github/workflows/npm-test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/npm-test.yml b/.github/workflows/npm-test.yml
index e8ea4c46..fa1fb316 100644
--- a/.github/workflows/npm-test.yml
+++ b/.github/workflows/npm-test.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node: ['16']
+        node: [16, 18, 20]
     name: node-${{ matrix.node }}
     steps:
       - uses: actions/checkout@v2

From 02d41ba804a343d76a2ddf9e8523cf81d1513553 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 6 Jan 2025 10:28:48 -0800
Subject: [PATCH 28/29] reverting some changes

---
 package-lock.json                | 557 ++++++++++++++++++++++---------
 package.json                     |   8 +-
 src/drugbank/index.js            |   5 +-
 test/civic/civic.profile.test.js |  24 +-
 4 files changed, 413 insertions(+), 181 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index cdc67ce9..618d4815 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -30,10 +30,11 @@
         "read-excel-file": "^5.2.28",
         "sleep-promise": "^8.0.1",
         "winston": "^3.2.1",
+        "xml-stream": "^0.4.5",
         "xml2js": "^0.6.2"
       },
       "devDependencies": {
-        "eslint": "8.17.0",
+        "eslint": "^8.17.0",
         "eslint-config-airbnb": "^19.0.4",
         "eslint-plugin-import": "^2.26.0",
         "eslint-plugin-jest": "^28.10.0",
@@ -675,15 +676,24 @@
         "eslint": "^6.0.0 || ^7.0.0 || >=8.0.0"
       }
     },
+    "node_modules/@eslint-community/regexpp": {
+      "version": "4.12.1",
+      "resolved": "https://registry.npmjs.org/@eslint-community/regexpp/-/regexpp-4.12.1.tgz",
+      "integrity": "sha512-CCZCDJuduB9OUkFkY2IgppNZMi2lBQgD2qzwXkEia16cge2pijY/aXi96CJMquDMn3nJdlPV1A5KrJEXwfLNzQ==",
+      "dev": true,
+      "engines": {
+        "node": "^12.0.0 || ^14.0.0 || >=16.0.0"
+      }
+    },
     "node_modules/@eslint/eslintrc": {
-      "version": "1.4.1",
-      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-1.4.1.tgz",
-      "integrity": "sha512-XXrH9Uarn0stsyldqDYq8r++mROmWRI1xKMXa640Bb//SY1+ECYX6VzT6Lcx5frD0V30XieqJ0oX9I2Xj5aoMA==",
+      "version": "2.1.4",
+      "resolved": "https://registry.npmjs.org/@eslint/eslintrc/-/eslintrc-2.1.4.tgz",
+      "integrity": "sha512-269Z39MS6wVJtsoUl10L60WdkhJVdPG24Q4eZTH3nnF6lpvSShEK3wQjDX9JRWAUPvPh7COouPpU9IrqaZFvtQ==",
       "dev": true,
       "dependencies": {
         "ajv": "^6.12.4",
         "debug": "^4.3.2",
-        "espree": "^9.4.0",
+        "espree": "^9.6.0",
         "globals": "^13.19.0",
         "ignore": "^5.2.0",
         "import-fresh": "^3.2.1",
@@ -698,6 +708,15 @@
         "url": "https://opencollective.com/eslint"
       }
     },
+    "node_modules/@eslint/js": {
+      "version": "8.57.1",
+      "resolved": "https://registry.npmjs.org/@eslint/js/-/js-8.57.1.tgz",
+      "integrity": "sha512-d9zaMRSTIKDLhctzH12MtXvJKSSUhaHcjV+2Z+GK+EEY7XKpP5yR4x+N3TAcHTcu963nIr+TMcCb4DBCYX1z6Q==",
+      "dev": true,
+      "engines": {
+        "node": "^12.22.0 || ^14.17.0 || >=16.0.0"
+      }
+    },
     "node_modules/@fast-csv/format": {
       "version": "4.3.5",
       "resolved": "https://registry.npmjs.org/@fast-csv/format/-/format-4.3.5.tgz",
@@ -736,24 +755,37 @@
       "integrity": "sha512-j11XSuRuAlft6vLDEX4RvhqC0KxNxx6QIyMXNb0vHHSNPXTPeiy3algESWmOOIzEtiEL0qiowPU3ewW9hHVa7Q=="
     },
     "node_modules/@humanwhocodes/config-array": {
-      "version": "0.9.5",
-      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.9.5.tgz",
-      "integrity": "sha512-ObyMyWxZiCu/yTisA7uzx81s40xR2fD5Cg/2Kq7G02ajkNubJf6BopgDTmDyc3U7sXpNKM8cYOw7s7Tyr+DnCw==",
+      "version": "0.13.0",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.13.0.tgz",
+      "integrity": "sha512-DZLEEqFWQFiyK6h5YIeynKx7JlvCYWL0cImfSRXZ9l4Sg2efkFGTuFf6vzXjK1cq6IYkU+Eg/JizXw+TD2vRNw==",
       "deprecated": "Use @eslint/config-array instead",
       "dev": true,
       "dependencies": {
-        "@humanwhocodes/object-schema": "^1.2.1",
-        "debug": "^4.1.1",
-        "minimatch": "^3.0.4"
+        "@humanwhocodes/object-schema": "^2.0.3",
+        "debug": "^4.3.1",
+        "minimatch": "^3.0.5"
       },
       "engines": {
         "node": ">=10.10.0"
       }
     },
+    "node_modules/@humanwhocodes/module-importer": {
+      "version": "1.0.1",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/module-importer/-/module-importer-1.0.1.tgz",
+      "integrity": "sha512-bxveV4V8v5Yb4ncFTT3rPSgZBOpCkjfK0y4oVVVJwIuDVBRMDXrPyXRL988i5ap9m9bnyEEjWfm5WkBmtffLfA==",
+      "dev": true,
+      "engines": {
+        "node": ">=12.22"
+      },
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/nzakas"
+      }
+    },
     "node_modules/@humanwhocodes/object-schema": {
-      "version": "1.2.1",
-      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-1.2.1.tgz",
-      "integrity": "sha512-ZnQMnLV4e7hDlUvw8H+U8ASL02SS2Gn6+9Ac3wGGLIe7+je2AeAOxPY+izIPJDfFDb7eDjev0Us8MO1iFRN8hA==",
+      "version": "2.0.3",
+      "resolved": "https://registry.npmjs.org/@humanwhocodes/object-schema/-/object-schema-2.0.3.tgz",
+      "integrity": "sha512-93zYdMES/c1D69yZiKDBj0V24vqNzB/koF26KPaagAfd3P/4gUlh3Dys5ogAK+Exi9QyzlD8x/08Zt7wIKcDcA==",
       "deprecated": "Use @eslint/object-schema instead",
       "dev": true
     },
@@ -2402,6 +2434,12 @@
         "url": "https://opencollective.com/typescript-eslint"
       }
     },
+    "node_modules/@ungap/structured-clone": {
+      "version": "1.2.1",
+      "resolved": "https://registry.npmjs.org/@ungap/structured-clone/-/structured-clone-1.2.1.tgz",
+      "integrity": "sha512-fEzPV3hSkSMltkw152tJKNARhOupqbH96MZWyRjNaYZOMIzbrTeQDG+MTc6Mr2pgzFQzFxAfmhGDNP5QK++2ZA==",
+      "dev": true
+    },
     "node_modules/@xmldom/xmldom": {
       "version": "0.8.6",
       "resolved": "https://registry.npmjs.org/@xmldom/xmldom/-/xmldom-0.8.6.tgz",
@@ -2890,6 +2928,14 @@
         "node": "*"
       }
     },
+    "node_modules/bindings": {
+      "version": "1.5.0",
+      "resolved": "https://registry.npmjs.org/bindings/-/bindings-1.5.0.tgz",
+      "integrity": "sha512-p2q/t/mhvuOj/UeLlV6566GD/guowlr0hHxClI0W9m7MWYkL1F0hLo+0Aexs9HSPCtR1SXQ0TD3MMKrXZajbiQ==",
+      "dependencies": {
+        "file-uri-to-path": "1.0.0"
+      }
+    },
     "node_modules/bluebird": {
       "version": "3.4.7",
       "resolved": "https://registry.npmjs.org/bluebird/-/bluebird-3.4.7.tgz",
@@ -3740,47 +3786,50 @@
       }
     },
     "node_modules/eslint": {
-      "version": "8.17.0",
-      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.17.0.tgz",
-      "integrity": "sha512-gq0m0BTJfci60Fz4nczYxNAlED+sMcihltndR8t9t1evnU/azx53x3t2UHXC/uRjcbvRw/XctpaNygSTcQD+Iw==",
+      "version": "8.57.1",
+      "resolved": "https://registry.npmjs.org/eslint/-/eslint-8.57.1.tgz",
+      "integrity": "sha512-ypowyDxpVSYpkXr9WPv2PAZCtNip1Mv5KTW0SCurXv/9iOpcrH9PaqUElksqEB6pChqHGDRCFTyrZlGhnLNGiA==",
       "deprecated": "This version is no longer supported. Please see https://eslint.org/version-support for other options.",
       "dev": true,
       "dependencies": {
-        "@eslint/eslintrc": "^1.3.0",
-        "@humanwhocodes/config-array": "^0.9.2",
-        "ajv": "^6.10.0",
+        "@eslint-community/eslint-utils": "^4.2.0",
+        "@eslint-community/regexpp": "^4.6.1",
+        "@eslint/eslintrc": "^2.1.4",
+        "@eslint/js": "8.57.1",
+        "@humanwhocodes/config-array": "^0.13.0",
+        "@humanwhocodes/module-importer": "^1.0.1",
+        "@nodelib/fs.walk": "^1.2.8",
+        "@ungap/structured-clone": "^1.2.0",
+        "ajv": "^6.12.4",
         "chalk": "^4.0.0",
         "cross-spawn": "^7.0.2",
         "debug": "^4.3.2",
         "doctrine": "^3.0.0",
         "escape-string-regexp": "^4.0.0",
-        "eslint-scope": "^7.1.1",
-        "eslint-utils": "^3.0.0",
-        "eslint-visitor-keys": "^3.3.0",
-        "espree": "^9.3.2",
-        "esquery": "^1.4.0",
+        "eslint-scope": "^7.2.2",
+        "eslint-visitor-keys": "^3.4.3",
+        "espree": "^9.6.1",
+        "esquery": "^1.4.2",
         "esutils": "^2.0.2",
         "fast-deep-equal": "^3.1.3",
         "file-entry-cache": "^6.0.1",
-        "functional-red-black-tree": "^1.0.1",
-        "glob-parent": "^6.0.1",
-        "globals": "^13.15.0",
+        "find-up": "^5.0.0",
+        "glob-parent": "^6.0.2",
+        "globals": "^13.19.0",
+        "graphemer": "^1.4.0",
         "ignore": "^5.2.0",
-        "import-fresh": "^3.0.0",
         "imurmurhash": "^0.1.4",
         "is-glob": "^4.0.0",
+        "is-path-inside": "^3.0.3",
         "js-yaml": "^4.1.0",
         "json-stable-stringify-without-jsonify": "^1.0.1",
         "levn": "^0.4.1",
         "lodash.merge": "^4.6.2",
         "minimatch": "^3.1.2",
         "natural-compare": "^1.4.0",
-        "optionator": "^0.9.1",
-        "regexpp": "^3.2.0",
+        "optionator": "^0.9.3",
         "strip-ansi": "^6.0.1",
-        "strip-json-comments": "^3.1.0",
-        "text-table": "^0.2.0",
-        "v8-compile-cache": "^2.0.3"
+        "text-table": "^0.2.0"
       },
       "bin": {
         "eslint": "bin/eslint.js"
@@ -4132,33 +4181,6 @@
         "node": ">=4.0"
       }
     },
-    "node_modules/eslint-utils": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-3.0.0.tgz",
-      "integrity": "sha512-uuQC43IGctw68pJA1RgbQS8/NP7rch6Cwd4j3ZBtgo4/8Flj4eGE7ZYSZRN3iq5pVUv6GPdW5Z1RFleo84uLDA==",
-      "dev": true,
-      "dependencies": {
-        "eslint-visitor-keys": "^2.0.0"
-      },
-      "engines": {
-        "node": "^10.0.0 || ^12.0.0 || >= 14.0.0"
-      },
-      "funding": {
-        "url": "https://github.com/sponsors/mysticatea"
-      },
-      "peerDependencies": {
-        "eslint": ">=5"
-      }
-    },
-    "node_modules/eslint-utils/node_modules/eslint-visitor-keys": {
-      "version": "2.1.0",
-      "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-2.1.0.tgz",
-      "integrity": "sha512-0rSmRBzXgDzIsD6mGdJgevzgezI534Cer5L/vyMX0kHzT/jiB43jRhd9YUlMGYLQy2zprNmoT8qasCGtY+QaKw==",
-      "dev": true,
-      "engines": {
-        "node": ">=10"
-      }
-    },
     "node_modules/eslint-visitor-keys": {
       "version": "3.4.3",
       "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz",
@@ -4253,6 +4275,22 @@
         "url": "https://github.com/sponsors/sindresorhus"
       }
     },
+    "node_modules/eslint/node_modules/find-up": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/find-up/-/find-up-5.0.0.tgz",
+      "integrity": "sha512-78/PXT1wlLLDgTzDs7sjq9hzz0vXD+zn+7wypEe4fXQxCmdmqfGsEPQxmiCSQI3ajFV91bVSsvNtrJRiW6nGng==",
+      "dev": true,
+      "dependencies": {
+        "locate-path": "^6.0.0",
+        "path-exists": "^4.0.0"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/eslint/node_modules/has-flag": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/has-flag/-/has-flag-4.0.0.tgz",
@@ -4275,6 +4313,21 @@
         "node": ">= 0.8.0"
       }
     },
+    "node_modules/eslint/node_modules/locate-path": {
+      "version": "6.0.0",
+      "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-6.0.0.tgz",
+      "integrity": "sha512-iPZK6eYjbxRu3uB4/WZ3EsEIMJFMqAoopl3R+zuq0UjcAm/MO6KCweDgPfP3elTztoKP3KtnVHxTn2NHBSDVUw==",
+      "dev": true,
+      "dependencies": {
+        "p-locate": "^5.0.0"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
     "node_modules/eslint/node_modules/optionator": {
       "version": "0.9.4",
       "resolved": "https://registry.npmjs.org/optionator/-/optionator-0.9.4.tgz",
@@ -4292,6 +4345,30 @@
         "node": ">= 0.8.0"
       }
     },
+    "node_modules/eslint/node_modules/p-locate": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/p-locate/-/p-locate-5.0.0.tgz",
+      "integrity": "sha512-LaNjtRWUBY++zB5nE/NwcaoMylSPk+S+ZHNB1TzdbMJMny6dynpAGt7X/tl/QYq3TIeE6nxHppbo2LGymrG5Pw==",
+      "dev": true,
+      "dependencies": {
+        "p-limit": "^3.0.2"
+      },
+      "engines": {
+        "node": ">=10"
+      },
+      "funding": {
+        "url": "https://github.com/sponsors/sindresorhus"
+      }
+    },
+    "node_modules/eslint/node_modules/path-exists": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/path-exists/-/path-exists-4.0.0.tgz",
+      "integrity": "sha512-ak9Qy5Q7jYb2Wwcey5Fpvg2KoAc/ZIhLSLOSBmRmygPsGwkVVt0fZa0qrtMz+m6tJTAHfZQ8FnmB4MG4LWy7/w==",
+      "dev": true,
+      "engines": {
+        "node": ">=8"
+      }
+    },
     "node_modules/eslint/node_modules/prelude-ls": {
       "version": "1.2.1",
       "resolved": "https://registry.npmjs.org/prelude-ls/-/prelude-ls-1.2.1.tgz",
@@ -4842,6 +4919,11 @@
         "node": "^10.12.0 || >=12.0.0"
       }
     },
+    "node_modules/file-uri-to-path": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
+      "integrity": "sha512-0Zt+s3L7Vf1biwWZ29aARiVYLx7iMGnEUl9x33fbB/j3jR81u/O2LbqK+Bm1CDSNDKVtJ/YjwY7TUd5SkeLQLw=="
+    },
     "node_modules/fill-range": {
       "version": "7.1.1",
       "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
@@ -4957,12 +5039,6 @@
         "url": "https://github.com/sponsors/ljharb"
       }
     },
-    "node_modules/functional-red-black-tree": {
-      "version": "1.0.1",
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       "requires": {
-        "@typescript-eslint/utils": "^7.0.0"
+        "@typescript-eslint/utils": "^6.0.0 || ^7.0.0 || ^8.0.0"
       },
       "dependencies": {
         "@typescript-eslint/utils": {
@@ -15361,23 +15561,6 @@
         }
       }
     },
-    "eslint-utils": {
-      "version": "3.0.0",
-      "resolved": "https://registry.npmjs.org/eslint-utils/-/eslint-utils-3.0.0.tgz",
-      "integrity": "sha512-uuQC43IGctw68pJA1RgbQS8/NP7rch6Cwd4j3ZBtgo4/8Flj4eGE7ZYSZRN3iq5pVUv6GPdW5Z1RFleo84uLDA==",
-      "dev": true,
-      "requires": {
-        "eslint-visitor-keys": "^2.0.0"
-      },
-      "dependencies": {
-        "eslint-visitor-keys": {
-          "version": "2.1.0",
-          "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-2.1.0.tgz",
-          "integrity": "sha512-0rSmRBzXgDzIsD6mGdJgevzgezI534Cer5L/vyMX0kHzT/jiB43jRhd9YUlMGYLQy2zprNmoT8qasCGtY+QaKw==",
-          "dev": true
-        }
-      }
-    },
     "eslint-visitor-keys": {
       "version": "3.4.3",
       "resolved": "https://registry.npmjs.org/eslint-visitor-keys/-/eslint-visitor-keys-3.4.3.tgz",
@@ -15741,6 +15924,11 @@
         "flat-cache": "^3.0.4"
       }
     },
+    "file-uri-to-path": {
+      "version": "1.0.0",
+      "resolved": "https://registry.npmjs.org/file-uri-to-path/-/file-uri-to-path-1.0.0.tgz",
+      "integrity": "sha512-0Zt+s3L7Vf1biwWZ29aARiVYLx7iMGnEUl9x33fbB/j3jR81u/O2LbqK+Bm1CDSNDKVtJ/YjwY7TUd5SkeLQLw=="
+    },
     "fill-range": {
       "version": "7.1.1",
       "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.1.1.tgz",
@@ -15827,12 +16015,6 @@
         "functions-have-names": "^1.2.2"
       }
     },
-    "functional-red-black-tree": {
-      "version": "1.0.1",
-      "resolved": "https://registry.npmjs.org/functional-red-black-tree/-/functional-red-black-tree-1.0.1.tgz",
-      "integrity": "sha512-dsKNQNdj6xA3T+QlADDA7mOSlX0qiMINjn0cgr+eGHGsbSHzTabcIogz2+p/iqP1Xs6EP/sS2SbqH+brGTbq0g==",
-      "dev": true
-    },
     "functions-have-names": {
       "version": "1.2.3",
       "resolved": "https://registry.npmjs.org/functions-have-names/-/functions-have-names-1.2.3.tgz",
@@ -15940,6 +16122,12 @@
       "resolved": "https://registry.npmjs.org/graceful-fs/-/graceful-fs-4.2.10.tgz",
       "integrity": "sha512-9ByhssR2fPVsNZj478qUUbKfmL0+t5BDVyjShtyZZLiK7ZDAArFFfopyOTj0M05wE2tJPisA4iTnnXl2YoPvOA=="
     },
+    "graphemer": {
+      "version": "1.4.0",
+      "resolved": "https://registry.npmjs.org/graphemer/-/graphemer-1.4.0.tgz",
+      "integrity": "sha512-EtKwoO6kxCL9WO5xipiHTZlSzBm7WLT627TqC/uVRd0HKmq8NXyebnNYxDoBi7wt8eTWrUrKXCOVaFq9x1kgag==",
+      "dev": true
+    },
     "has": {
       "version": "1.0.3",
       "resolved": "https://registry.npmjs.org/has/-/has-1.0.3.tgz",
@@ -16090,6 +16278,15 @@
       "integrity": "sha512-B4FFZ6q/T2jhhksgkbEW3HBvWIfDW85snkQgawt07S7J5QXTk6BkNV+0yAeZrM5QpMAdYlocGoljn0sJ/WQkFw==",
       "dev": true
     },
+    "iconv": {
+      "version": "2.3.5",
+      "resolved": "https://registry.npmjs.org/iconv/-/iconv-2.3.5.tgz",
+      "integrity": "sha512-U5ajDbtDfadp7pvUMC0F2XbkP5vQn9Xrwa6UptePl+cK8EILxapAt3sXers9B3Gxagk+zVjL2ELKuzQvyqOwug==",
+      "requires": {
+        "nan": "^2.14.0",
+        "safer-buffer": "^2.1.2"
+      }
+    },
     "iconv-lite": {
       "version": "0.4.24",
       "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.4.24.tgz",
@@ -16316,6 +16513,12 @@
         "has-tostringtag": "^1.0.0"
       }
     },
+    "is-path-inside": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/is-path-inside/-/is-path-inside-3.0.3.tgz",
+      "integrity": "sha512-Fd4gABb+ycGAmKou8eMftCupSir5lRxqf4aD/vd0cD2qc4HL07OjCeuHMr8Ro4CoMaeCKDB0/ECBOVWjTwUvPQ==",
+      "dev": true
+    },
     "is-potential-custom-element-name": {
       "version": "1.0.1",
       "resolved": "https://registry.npmjs.org/is-potential-custom-element-name/-/is-potential-custom-element-name-1.0.1.tgz",
@@ -19865,12 +20068,26 @@
         }
       }
     },
+    "nan": {
+      "version": "2.22.0",
+      "resolved": "https://registry.npmjs.org/nan/-/nan-2.22.0.tgz",
+      "integrity": "sha512-nbajikzWTMwsW+eSsNm3QwlOs7het9gGJU5dDZzRTQGk03vyBOauxgI4VakDzE0PtsGTmXPsXTbbjVhRwR5mpw=="
+    },
     "natural-compare": {
       "version": "1.4.0",
       "resolved": "https://registry.npmjs.org/natural-compare/-/natural-compare-1.4.0.tgz",
       "integrity": "sha1-Sr6/7tdUHywnrPspvbvRXI1bpPc=",
       "dev": true
     },
+    "node-expat": {
+      "version": "2.4.1",
+      "resolved": "https://registry.npmjs.org/node-expat/-/node-expat-2.4.1.tgz",
+      "integrity": "sha512-uWgvQLgo883NKIL+66oJsK9ysKK3ej0YjVCPBZzO/7wMAuH68/Yb7+JwPWNaVq0yPaxrb48AoEXfYEc8gsmFbg==",
+      "requires": {
+        "bindings": "^1.5.0",
+        "nan": "^2.19.0"
+      }
+    },
     "node-fetch": {
       "version": "2.6.7",
       "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz",
@@ -20295,12 +20512,6 @@
         "functions-have-names": "^1.2.2"
       }
     },
-    "regexpp": {
-      "version": "3.2.0",
-      "resolved": "https://registry.npmjs.org/regexpp/-/regexpp-3.2.0.tgz",
-      "integrity": "sha512-pq2bWo9mVD43nbts2wGv17XLiNLya+GklZ8kaDLV2Z08gDCsGpnKn9BFMepvWuHCbyVvY7J5o5+BVvoQbmlJLg==",
-      "dev": true
-    },
     "require-directory": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -20382,8 +20593,7 @@
     "safer-buffer": {
       "version": "2.1.2",
       "resolved": "https://registry.npmjs.org/safer-buffer/-/safer-buffer-2.1.2.tgz",
-      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg==",
-      "dev": true
+      "integrity": "sha512-YZo3K82SD7Riyi0E1EQPojLz7kpepnSQI9IyPbHHg1XXXevb5dJI7tpyN2ADxGcQbHG7vcyRHk0cbwqcQriUtg=="
     },
     "sax": {
       "version": "1.2.4",
@@ -20937,12 +21147,6 @@
       "resolved": "https://registry.npmjs.org/uuid-validate/-/uuid-validate-0.0.3.tgz",
       "integrity": "sha512-Fykw5U4eZESbq739BeLvEBFRuJODfrlmjx5eJux7W817LjRaq4b7/i4t2zxQmhcX+fAj4nMfRdTzO4tmwLKn0w=="
     },
-    "v8-compile-cache": {
-      "version": "2.4.0",
-      "resolved": "https://registry.npmjs.org/v8-compile-cache/-/v8-compile-cache-2.4.0.tgz",
-      "integrity": "sha512-ocyWc3bAHBB/guyqJQVI5o4BZkPhznPYUG2ea80Gond/BgNWpap8TOmLSeeQG7bnh2KMISxskdADG59j7zruhw==",
-      "dev": true
-    },
     "v8-to-istanbul": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/v8-to-istanbul/-/v8-to-istanbul-8.1.0.tgz",
@@ -21223,6 +21427,39 @@
       "integrity": "sha512-A5CUptxDsvxKJEU3yO6DuWBSJz/qizqzJKOMIfUJHETbBw/sFaDxgd6fxm1ewUaM0jZ444Fc5vC5ROYurg/4Pw==",
       "dev": true
     },
+    "xml-stream": {
+      "version": "0.4.5",
+      "resolved": "https://registry.npmjs.org/xml-stream/-/xml-stream-0.4.5.tgz",
+      "integrity": "sha512-WdMVMiYgJ2UQO2vs8CRVOd0CD0GW3AfeWHwpFJWB+bRYbnNNn88BxoYbjm0qRijceJgP1krCRwr6DgfbQKudmA==",
+      "requires": {
+        "iconv": "^2.1.4",
+        "node-expat": "^2.3.1",
+        "readable-stream": "^1.0.31"
+      },
+      "dependencies": {
+        "isarray": {
+          "version": "0.0.1",
+          "resolved": "https://registry.npmjs.org/isarray/-/isarray-0.0.1.tgz",
+          "integrity": "sha512-D2S+3GLxWH+uhrNEcoh/fnmYeP8E8/zHl644d/jdA0g2uyXvy3sb0qxotE+ne0LtccHknQzWwZEzhak7oJ0COQ=="
+        },
+        "readable-stream": {
+          "version": "1.1.14",
+          "resolved": "https://registry.npmjs.org/readable-stream/-/readable-stream-1.1.14.tgz",
+          "integrity": "sha512-+MeVjFf4L44XUkhM1eYbD8fyEsxcV81pqMSR5gblfcLCHfZvbrqy4/qYHE+/R5HoBUT11WV5O08Cr1n3YXkWVQ==",
+          "requires": {
+            "core-util-is": "~1.0.0",
+            "inherits": "~2.0.1",
+            "isarray": "0.0.1",
+            "string_decoder": "~0.10.x"
+          }
+        },
+        "string_decoder": {
+          "version": "0.10.31",
+          "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
+          "integrity": "sha512-ev2QzSzWPYmy9GuqfIVildA4OdcGLeFZQrq5ys6RtiuF+RQQiZWr8TZNyAcuVXyQRYfEO+MsoB/1BuQVhOJuoQ=="
+        }
+      }
+    },
     "xml2js": {
       "version": "0.6.2",
       "resolved": "https://registry.npmjs.org/xml2js/-/xml2js-0.6.2.tgz",
diff --git a/package.json b/package.json
index 10ad395b..2627a7ec 100644
--- a/package.json
+++ b/package.json
@@ -33,10 +33,11 @@
     "read-excel-file": "^5.2.28",
     "sleep-promise": "^8.0.1",
     "winston": "^3.2.1",
+    "xml-stream": "^0.4.5",
     "xml2js": "^0.6.2"
   },
   "devDependencies": {
-    "eslint": "8.17.0",
+    "eslint": "^8.17.0",
     "eslint-config-airbnb": "^19.0.4",
     "eslint-plugin-import": "^2.26.0",
     "eslint-plugin-jest": "^28.10.0",
@@ -51,11 +52,6 @@
     "jest-circus": "^27.3.1",
     "jest-junit": "^13.0.0"
   },
-  "overrides": {
-    "eslint-plugin-jest": {
-      "@typescript-eslint/utils": "^7.0.0"
-    }
-  },
   "scripts": {
     "test": "NODE_ENV=test jest --config config/jest.config.js",
     "lint": "eslint -c .eslintrc.json src test",
diff --git a/src/drugbank/index.js b/src/drugbank/index.js
index 877b8e94..d3a37904 100644
--- a/src/drugbank/index.js
+++ b/src/drugbank/index.js
@@ -4,7 +4,7 @@
  */
 
 const Ajv = require('ajv');
-// const XmlStream = require('xml-stream');
+const XmlStream = require('xml-stream');
 const fs = require('fs');
 
 const { checkSpec } = require('../util');
@@ -279,8 +279,7 @@ const uploadFile = async ({ filename, conn, maxRecords }) => {
     const parseXML = new Promise((resolve, reject) => {
         logger.log('info', `loading XML data from ${filename}`);
         const stream = fs.createReadStream(filename);
-        // const xml = new XmlStream(stream);
-        const xml = {};
+        const xml = new XmlStream(stream);
         xml.collect('drug drugbank-id');
         xml.collect('drug external-identifier');
         xml.collect('drug synonym');
diff --git a/test/civic/civic.profile.test.js b/test/civic/civic.profile.test.js
index 752df4dc..ee8ea60d 100644
--- a/test/civic/civic.profile.test.js
+++ b/test/civic/civic.profile.test.js
@@ -226,16 +226,16 @@ describe('MolecularProfile.process()', () => {
         );
     });
 
-    // test('test case that should throw a NotImplementedError', () => {
-    //     const molecularProfile = {
-    //         id: 1,
-    //         parsedName: [
-    //             { __typename: 'Feature' }, { id: 1 }, { text: 'AND' }, { text: 'NOT' }, { text: '(' },
-    //             { __typename: 'Feature' }, { id: 2 }, { text: 'OR' }, { __typename: 'Feature' }, { id: 3 }, { text: ')' },
-    //         ],
-    //     };
-    //     expect(() => MolecularProfile(molecularProfile).process()).toThrow(
-    //         `unable to process molecular profile with NOT operator (${molecularProfile.id || ''})`,
-    //     );
-    // });
+    test('test case that should throw a NotImplementedError', () => {
+        const molecularProfile = {
+            id: 1,
+            parsedName: [
+                { __typename: 'Feature' }, { id: 1 }, { text: 'AND' }, { text: 'NOT' }, { text: '(' },
+                { __typename: 'Feature' }, { id: 2 }, { text: 'OR' }, { __typename: 'Feature' }, { id: 3 }, { text: ')' },
+            ],
+        };
+        expect(() => MolecularProfile(molecularProfile).process()).toThrow(
+            `unable to process molecular profile with NOT operator (${molecularProfile.id || ''})`,
+        );
+    });
 });

From eb9f0902b86826382a3e184711725e25da72c4e6 Mon Sep 17 00:00:00 2001
From: mathieulemieux <mathieu@mathieulemieux.com>
Date: Mon, 6 Jan 2025 10:34:52 -0800
Subject: [PATCH 29/29] Fix test title

---
 test/civic/civic.profile.test.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/civic/civic.profile.test.js b/test/civic/civic.profile.test.js
index ee8ea60d..d1ea8e9b 100644
--- a/test/civic/civic.profile.test.js
+++ b/test/civic/civic.profile.test.js
@@ -226,7 +226,7 @@ describe('MolecularProfile.process()', () => {
         );
     });
 
-    test('test case that should throw a NotImplementedError', () => {
+    test('Case that should throw a NotImplementedError', () => {
         const molecularProfile = {
             id: 1,
             parsedName: [