From b9e137605ff70f060ad79f28244b928bd1badf40 Mon Sep 17 00:00:00 2001
From: Caralyn Reisle <creisle@users.noreply.github.com>
Date: Thu, 15 Apr 2021 15:37:16 -0700
Subject: [PATCH 01/23] Add link to main PORI repo

---
 README.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/README.md b/README.md
index 5e0de327..377852f4 100644
--- a/README.md
+++ b/README.md
@@ -2,6 +2,8 @@
 
 ![build](https://github.com/bcgsc/pori_graphkb_loader/workflows/build/badge.svg?branch=master) ![Docker Image Version (latest semver)](https://img.shields.io/docker/v/bcgsc/pori-graphkb-loader?label=docker%20image) ![node versions](https://img.shields.io/badge/node-10%20%7C%2012%20%7C%2014-blue)
 
+This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori).
+
 This package is used to import content from a variety of sources into GraphKB using the API.
 
 - [Loaders](#loaders)

From 9adc76aff55289ce421b4cfbae7c7f3a0670456c Mon Sep 17 00:00:00 2001
From: Caralyn Reisle <creisle@bcgsc.ca>
Date: Fri, 16 Apr 2021 11:39:56 -0700
Subject: [PATCH 02/23] Improve doc strings

---
 src/civic/index.js   |  1 +
 src/civic/variant.js |  4 ++-
 src/graphkb.js       | 59 ++++++++++++++++++++++++++++++++++++++------
 3 files changed, 56 insertions(+), 8 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 01fb22af..346032c4 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -682,6 +682,7 @@ const upload = async (opt) => {
 
         const oneToOne = mappedCount === 1 && preupload.size === 1;
 
+        // upload all GraphKB statements for this CIViC Evidence Item
         for (const record of recordList) {
             for (const variant of record.variants) {
                 for (const drugs of record.drugs) {
diff --git a/src/civic/variant.js b/src/civic/variant.js
index f55ec0b7..df131f3e 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -133,6 +133,7 @@ const normalizeVariantRecord = ({
             type: name.replace(/-/g, ' '),
         }];
     } if (match = /^t\(([^;()]+);([^;()]+)\)\(([^;()]+);([^;()]+)\)$/i.exec(name)) {
+        // convert translocation syntax
         const [, chr1, chr2, pos1, pos2] = match;
         return [{
             positional: true,
@@ -141,6 +142,7 @@ const normalizeVariantRecord = ({
             variant: `translocation(${pos1}, ${pos2})`,
         }];
     } if (match = /^(p\.)?([a-z*]\d+\S*)\s+\((c\.[^)]+)\)$/i.exec(name)) {
+        // split combined protein + cds notation
         let [, , protein, cds] = match;
 
         // correct deprecated cds syntac
@@ -152,7 +154,7 @@ const normalizeVariantRecord = ({
             }
         }
         return [{
-            inferredBy: [
+            inferredBy: [ // keep the cds variant as a link to the protein variant
                 {
                     positional: true,
                     reference1: { ...referenceGene },
diff --git a/src/graphkb.js b/src/graphkb.js
index 18b8358d..55d66247 100644
--- a/src/graphkb.js
+++ b/src/graphkb.js
@@ -45,7 +45,14 @@ const simplifyRecordsLinks = (content, level = 0) => {
     return content;
 };
 
-
+/**
+ * Check if things have changed and we should send an update request
+ *
+ * @param {string|ClassModel} modelIn the model name or model object this record belongs to
+ * @param {Object} originalContentIn the original record
+ * @param {Object} newContentIn the new record
+ * @param {string[]} upsertCheckExclude a list of properties to ignore changes in
+ */
 const shouldUpdate = (modelIn, originalContentIn, newContentIn, upsertCheckExclude = []) => {
     const model = typeof modelIn === 'string'
         ? schema.get(modelIn)
@@ -290,6 +297,15 @@ class ApiConnection {
         return created;
     }
 
+    /**
+     * Given some query, fetch all matching records (handles paginating over large queries)
+     * @param {Object} opt
+     * @param {Object} opt.filters query filters
+     * @param {string} opt.target the target class to be queried
+     * @param {Number} opt.limit maximum number of records to fetch per request
+     * @param {Number} opt.neighbors maximum record depth to fetch
+     * @param {string[]} opt.returnProperties properties to return from each record
+     */
     async getRecords(opt) {
         const {
             filters,
@@ -333,11 +349,16 @@ class ApiConnection {
     }
 
     /**
+     * Fetch a record with a query. Error if the record cannot be uniquely identified.
      *
-     * @param {object} opt
-     * @param {object} opt.filters the conditions/query parameters for the selection
-     * @param {string} opt.target the target to query
-     * @param {function} opt.sort the function to use in sorting if multiple results are found
+     * @param {Object} opt
+     * @param {Object} opt.filters query filters
+     * @param {string} opt.target the target class to be queried
+     * @param {Number} opt.limit maximum number of records to fetch per request
+     * @param {Number} opt.neighbors maximum record depth to fetch
+     * @param {function} opt.sort the comparator function to use in sorting if multiple results are found
+     *
+     * @throws on multiple records matching the query that do not have a non-zero sort comparison value
      */
     async getUniqueRecordBy(opt) {
         const {
@@ -367,6 +388,9 @@ class ApiConnection {
 
     /**
      * Fetch therapy by name, ignore plurals for some cases
+     *
+     * @param {string} term the name or sourceId of the therapeutic term
+     * @param {string} source the source record ID the therapy is expected to belong to
      */
     async getTherapy(term, source) {
         let error,
@@ -421,6 +445,10 @@ class ApiConnection {
         throw error;
     }
 
+    /**
+     * @param {string} term the name of the vocabulary term to be fetched
+     * @param {string} sourceName the name of the source the vocabulary term belongs to
+     */
     async getVocabularyTerm(term, sourceName = INTERNAL_SOURCE_NAME) {
         if (!term) {
             throw new Error('Cannot fetch vocabulary for empty term name');
@@ -452,6 +480,12 @@ class ApiConnection {
         return result;
     }
 
+    /**
+     * This will soft-delete a record via the API
+     *
+     * @param {string} target the class this record belongs to
+     * @param {string} recordId the ID of the record being deleted
+     */
     async deleteRecord(target, recordId) {
         const model = schema.get(target);
         const { result } = jc.retrocycle(await this.request({
@@ -540,8 +574,8 @@ class ApiConnection {
 
     /**
      * @param {object} opt
-     * @param {object} opt.content
-     * @param {string} opt.target
+     * @param {object} opt.content the content of the variant record
+     * @param {string} opt.target the class to add the record to (PositionalVariant or CategoryVariant)
      */
     async addVariant(opt) {
         const {
@@ -574,6 +608,17 @@ class ApiConnection {
         });
     }
 
+    /**
+     * Add a therapy combination. Will split the input name by "+" and query to find individual
+     * components. These will they be used to create the combination record
+     *
+     * TODO: link elements to combination therapy
+     *
+     * @param {string|Object} source the source record ID or source record this therapy belongs to
+     * @param {string} therapyName the name of the therpeutic combination
+     * @param {Object} opt
+     * @param {boolean} opt.matchSource flag to indicate sub-components of the therapy must be from the same source
+     */
     async addTherapyCombination(source, therapyName, opt = {}) {
         const { matchSource = false } = opt;
 

From a1cd83117693f3591549852e32a40d81d76eafad Mon Sep 17 00:00:00 2001
From: Caralyn Reisle <creisle@bcgsc.ca>
Date: Wed, 5 May 2021 15:48:22 -0700
Subject: [PATCH 03/23] Add tests for translateRelevance

---
 package-lock.json  |  41 ++++++++++++-----
 src/civic/index.js | 112 +++++++++++++++++++++++----------------------
 test/civic.test.js |  30 +++++++++++-
 3 files changed, 117 insertions(+), 66 deletions(-)

diff --git a/package-lock.json b/package-lock.json
index 1096b450..75073f36 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -887,7 +887,8 @@
           "version": "5.0.0",
           "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-5.0.0.tgz",
           "integrity": "sha512-qYg9KP24dD5qka9J47d0aVky0N+b4fTU89LN9iDnjB5waksiC49rvMB0PrUJQGoTmH50XPiqOvAjDfaijGxYZw==",
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "supports-color": {
           "version": "7.1.0",
@@ -4115,7 +4116,8 @@
         "ansi-regex": {
           "version": "2.1.1",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "aproba": {
           "version": "1.2.0",
@@ -4158,7 +4160,8 @@
         "code-point-at": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "concat-map": {
           "version": "0.0.1",
@@ -4169,7 +4172,8 @@
         "console-control-strings": {
           "version": "1.1.0",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "core-util-is": {
           "version": "1.0.2",
@@ -4286,7 +4290,8 @@
         "inherits": {
           "version": "2.0.4",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "ini": {
           "version": "1.3.5",
@@ -4298,6 +4303,7 @@
           "version": "1.0.0",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "number-is-nan": "^1.0.0"
           }
@@ -4320,12 +4326,14 @@
         "minimist": {
           "version": "1.2.5",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "minipass": {
           "version": "2.9.0",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "safe-buffer": "^5.1.2",
             "yallist": "^3.0.0"
@@ -4344,6 +4352,7 @@
           "version": "0.5.3",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "minimist": "^1.2.5"
           }
@@ -4434,7 +4443,8 @@
         "number-is-nan": {
           "version": "1.0.1",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "object-assign": {
           "version": "4.1.1",
@@ -4446,6 +4456,7 @@
           "version": "1.4.0",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "wrappy": "1"
           }
@@ -4523,7 +4534,8 @@
         "safe-buffer": {
           "version": "5.1.2",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "safer-buffer": {
           "version": "2.1.2",
@@ -4559,6 +4571,7 @@
           "version": "1.0.2",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "code-point-at": "^1.0.0",
             "is-fullwidth-code-point": "^1.0.0",
@@ -4578,6 +4591,7 @@
           "version": "3.0.1",
           "bundled": true,
           "dev": true,
+          "optional": true,
           "requires": {
             "ansi-regex": "^2.0.0"
           }
@@ -4621,12 +4635,14 @@
         "wrappy": {
           "version": "1.0.2",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         },
         "yallist": {
           "version": "3.1.1",
           "bundled": true,
-          "dev": true
+          "dev": true,
+          "optional": true
         }
       }
     },
@@ -5010,6 +5026,7 @@
       "resolved": "https://registry.npmjs.org/import-fresh/-/import-fresh-3.2.1.tgz",
       "integrity": "sha512-6e1q1cnWP2RXD9/keSkxHScg508CdXqXWgWBaETNhyuBFz+kUZlKboh+ISK+bU++DmbHimVBrOz/zzPe0sZ3sQ==",
       "dev": true,
+      "optional": true,
       "requires": {
         "parent-module": "^1.0.0",
         "resolve-from": "^4.0.0"
@@ -5019,7 +5036,8 @@
           "version": "4.0.0",
           "resolved": "https://registry.npmjs.org/resolve-from/-/resolve-from-4.0.0.tgz",
           "integrity": "sha512-pb/MYmXstAkysRFx8piNI1tGFNQIFA3vkE3Gq4EuA1dF6gHp/+vgZqsCGJapvy8N3Q+4o7FwvquPJcnZ7RYy4g==",
-          "dev": true
+          "dev": true,
+          "optional": true
         }
       }
     },
@@ -8546,6 +8564,7 @@
       "resolved": "https://registry.npmjs.org/parent-module/-/parent-module-1.0.1.tgz",
       "integrity": "sha512-GQ2EWRpQV8/o+Aw8YqtfZZPfNRWZYkbidE9k5rpl/hC3vtHHBfGm2Ifi6qWV+coDGkrUKZAxE3Lot5kcsRlh+g==",
       "dev": true,
+      "optional": true,
       "requires": {
         "callsites": "^3.0.0"
       }
diff --git a/src/civic/index.js b/src/civic/index.js
index 346032c4..e8db3783 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -112,78 +112,81 @@ const validateEvidenceSpec = ajv.compile({
 
 
 /**
- * Convert the CIViC relevance types to GraphKB terms
+ * Extract the appropriate GraphKB relevance term from a CIViC evidence record
  */
-const getRelevance = async ({ rawRecord, conn }) => {
-    const translateRelevance = ({ evidenceType, clinicalSignificance, evidenceDirection }) => {
-        switch (evidenceType) { // eslint-disable-line default-case
-            case 'Predictive': {
-                switch (clinicalSignificance) { // eslint-disable-line default-case
-                    case 'Sensitivity':
-                    case 'Adverse Response':
-                    case 'Reduced Sensitivity':
-
-                    case 'Resistance': {
-                        return clinicalSignificance.toLowerCase();
-                    }
-
-                    case 'Sensitivity/Response': { return 'sensitivity'; }
+const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificance) => {
+    switch (evidenceType) { // eslint-disable-line default-case
+        case 'Predictive': {
+            switch (clinicalSignificance) { // eslint-disable-line default-case
+                case 'Sensitivity':
+                case 'Adverse Response':
+                case 'Reduced Sensitivity':
+
+                case 'Resistance': {
+                    return clinicalSignificance.toLowerCase();
                 }
-                break;
-            }
 
-            case 'Functional': {
-                return clinicalSignificance.toLowerCase();
+                case 'Sensitivity/Response': { return 'sensitivity'; }
             }
+            break;
+        }
 
-            case 'Diagnostic': {
-                switch (clinicalSignificance) { // eslint-disable-line default-case
-                    case 'Positive': { return 'favours diagnosis'; }
+        case 'Functional': {
+            return clinicalSignificance.toLowerCase();
+        }
 
-                    case 'Negative': { return 'opposes diagnosis'; }
-                }
-                break;
+        case 'Diagnostic': {
+            switch (clinicalSignificance) { // eslint-disable-line default-case
+                case 'Positive': { return 'favours diagnosis'; }
+
+                case 'Negative': { return 'opposes diagnosis'; }
             }
+            break;
+        }
 
-            case 'Prognostic': {
-                switch (clinicalSignificance) { // eslint-disable-line default-case
-                    case 'Negative':
+        case 'Prognostic': {
+            switch (clinicalSignificance) { // eslint-disable-line default-case
+                case 'Negative':
 
-                    case 'Poor Outcome': {
-                        return 'unfavourable prognosis';
-                    }
-                    case 'Positive':
+                case 'Poor Outcome': {
+                    return 'unfavourable prognosis';
+                }
+                case 'Positive':
 
-                    case 'Better Outcome': {
-                        return 'favourable prognosis';
-                    }
+                case 'Better Outcome': {
+                    return 'favourable prognosis';
                 }
-                break;
             }
+            break;
+        }
 
-            case 'Predisposing': {
-                if (['Positive', null, 'null'].includes(clinicalSignificance)) {
-                    return 'Predisposing';
-                } if (clinicalSignificance.includes('Pathogenic')) {
-                    return clinicalSignificance;
-                } if (clinicalSignificance === 'Uncertain Significance') {
-                    return 'likely predisposing';
-                }
-                break;
+        case 'Predisposing': {
+            if (['Positive', null, 'null'].includes(clinicalSignificance)) {
+                return 'predisposing';
+            } if (clinicalSignificance.includes('Pathogenic')) {
+                return clinicalSignificance.toLowerCase();
+            } if (clinicalSignificance === 'Uncertain Significance') {
+                return 'likely predisposing';
             }
+            break;
         }
+    }
 
-        throw new Error(
-            `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
-        );
-    };
+    throw new Error(
+        `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
+    );
+};
 
+/**
+ * Convert the CIViC relevance types to GraphKB terms
+ */
+const getRelevance = async ({ rawRecord, conn }) => {
     // translate the type to a GraphKB vocabulary term
-    let relevance = translateRelevance({
-        clinicalSignificance: rawRecord.clinical_significance,
-        evidenceDirection: rawRecord.evidence_direction,
-        evidenceType: rawRecord.evidence_type,
-    }).toLowerCase();
+    let relevance = translateRelevance(
+        rawRecord.evidence_type,
+        rawRecord.evidence_direction,
+        rawRecord.clinical_significance,
+    ).toLowerCase();
 
     if (RELEVANCE_CACHE[relevance] === undefined) {
         relevance = await conn.getVocabularyTerm(relevance);
@@ -739,5 +742,6 @@ const upload = async (opt) => {
 module.exports = {
     SOURCE_DEFN,
     specs: { validateEvidenceSpec },
+    translateRelevance,
     upload,
 };
diff --git a/test/civic.test.js b/test/civic.test.js
index dab721c1..2662ff3a 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -1,5 +1,5 @@
 const { normalizeVariantRecord } = require('../src/civic/variant');
-
+const { translateRelevance } = require('../src/civic');
 
 describe('normalizeVariantRecord', () => {
     test('exon mutation', () => {
@@ -615,3 +615,31 @@ describe('normalizeVariantRecord', () => {
         });
     });
 });
+
+describe('translateRelevance', () => {
+    test.each([
+        ['Predictive', 'Supports', 'Sensitivity', 'sensitivity'],
+        ['Predictive', 'Supports', 'Adverse Response', 'adverse response'],
+        ['Predictive', 'Supports', 'Reduced Sensitivity', 'reduced sensitivity'],
+        ['Predictive', 'Supports', 'Resistance', 'resistance'],
+        ['Predictive', 'Supports', 'Sensitivity/Response', 'sensitivity'],
+        ['Diagnostic', 'Supports', 'Positive', 'favours diagnosis'],
+        ['Diagnostic', 'Supports', 'Negative', 'opposes diagnosis'],
+        ['Prognostic', 'Supports', 'Negative', 'unfavourable prognosis'],
+        ['Prognostic', 'Supports', 'Poor Outcome', 'unfavourable prognosis'],
+        ['Prognostic', 'Supports', 'Positive', 'favourable prognosis'],
+        ['Prognostic', 'Supports', 'Better Outcome', 'favourable prognosis'],
+        ['Predisposing', 'Supports', 'Positive', 'predisposing'],
+        ['Predisposing', 'Supports', null, 'predisposing'],
+        ['Predisposing', 'Supports', 'null', 'predisposing'],
+        ['Predisposing', 'Supports', 'Pathogenic', 'pathogenic'],
+        ['Predisposing', 'Supports', 'Likely Pathogenic', 'likely pathogenic'],
+        ['Functional', 'Supports', 'Gain of Function', 'gain of function'],
+        // ['Predictive', 'Does not Support', 'Sensitivity', 'no response'],
+        // ['Predictive', 'Does not Support', 'Sensitivity/Response', 'no response'],
+    ])(
+        '%s|%s|%s returns %s', (evidenceType, evidenceDirection, clinicalSignificance, expected) => {
+            expect(translateRelevance(evidenceType, evidenceDirection, clinicalSignificance)).toEqual(expected);
+        },
+    );
+});

From 4dd85092c29ab30886fa76a0d4a24def6f63cde3 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 10:45:03 -0700
Subject: [PATCH 04/23] Un-comment Predictive Does not Support test lines

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

diff --git a/test/civic.test.js b/test/civic.test.js
index 2662ff3a..9912a894 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -635,8 +635,8 @@ describe('translateRelevance', () => {
         ['Predisposing', 'Supports', 'Pathogenic', 'pathogenic'],
         ['Predisposing', 'Supports', 'Likely Pathogenic', 'likely pathogenic'],
         ['Functional', 'Supports', 'Gain of Function', 'gain of function'],
-        // ['Predictive', 'Does not Support', 'Sensitivity', 'no response'],
-        // ['Predictive', 'Does not Support', 'Sensitivity/Response', 'no response'],
+        ['Predictive', 'Does not Support', 'Sensitivity', 'no response'],
+        ['Predictive', 'Does not Support', 'Sensitivity/Response', 'no response'],
     ])(
         '%s|%s|%s returns %s', (evidenceType, evidenceDirection, clinicalSignificance, expected) => {
             expect(translateRelevance(evidenceType, evidenceDirection, clinicalSignificance)).toEqual(expected);

From 5335480c2bc337f38102de4cbda3245839e86b47 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 11:06:01 -0700
Subject: [PATCH 05/23] modify translateRelevance to support Does Not Support
 Sensitivity

---
 src/civic/index.js | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index e8db3783..4c0b5d05 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -119,6 +119,11 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
         case 'Predictive': {
             switch (clinicalSignificance) { // eslint-disable-line default-case
                 case 'Sensitivity':
+                    switch (evidenceDirection) {
+                        case 'Does Not Support': { return 'no response'; }
+                        case 'Supports': { return clinicalSignificance.toLowerCase(); }
+                    }
+
                 case 'Adverse Response':
                 case 'Reduced Sensitivity':
 
@@ -126,7 +131,12 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                     return clinicalSignificance.toLowerCase();
                 }
 
-                case 'Sensitivity/Response': { return 'sensitivity'; }
+                case 'Sensitivity/Response':
+                    switch (evidenceDirection) {
+                        case 'Does Not Support': { return 'no response'; }
+                        case 'Supports': { return 'sensitivity'; }
+                    }
+
             }
             break;
         }

From e0824185dc2b0cb82bbe68e924c2da7c99714918 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 11:13:09 -0700
Subject: [PATCH 06/23] fixing eslint errors

---
 src/civic/index.js | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 4c0b5d05..d564edc2 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -119,24 +119,21 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
         case 'Predictive': {
             switch (clinicalSignificance) { // eslint-disable-line default-case
                 case 'Sensitivity':
-                    switch (evidenceDirection) {
+                    switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
                         case 'Supports': { return clinicalSignificance.toLowerCase(); }
                     }
-
                 case 'Adverse Response':
                 case 'Reduced Sensitivity':
 
                 case 'Resistance': {
                     return clinicalSignificance.toLowerCase();
                 }
-
                 case 'Sensitivity/Response':
-                    switch (evidenceDirection) {
+                    switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
                         case 'Supports': { return 'sensitivity'; }
                     }
-
             }
             break;
         }

From 5747295ec35e7a3aaa5284054fd0bdf952a1348d Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 11:43:10 -0700
Subject: [PATCH 07/23] missing parentheses

---
 src/civic/index.js | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index d564edc2..692f69bf 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -118,22 +118,24 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
     switch (evidenceType) { // eslint-disable-line default-case
         case 'Predictive': {
             switch (clinicalSignificance) { // eslint-disable-line default-case
-                case 'Sensitivity':
+                case 'Sensitivity': {
                     switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
                         case 'Supports': { return clinicalSignificance.toLowerCase(); }
                     }
+                }
                 case 'Adverse Response':
                 case 'Reduced Sensitivity':
 
                 case 'Resistance': {
                     return clinicalSignificance.toLowerCase();
                 }
-                case 'Sensitivity/Response':
+                case 'Sensitivity/Response': {
                     switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
                         case 'Supports': { return 'sensitivity'; }
                     }
+                }
             }
             break;
         }

From ecbdcd3b918b2ba08e246cc8534f181c6be178ee Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 11:57:08 -0700
Subject: [PATCH 08/23] missing blank lines

---
 src/civic/index.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/civic/index.js b/src/civic/index.js
index 692f69bf..4fde141f 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -121,10 +121,12 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                 case 'Sensitivity': {
                     switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
+
                         case 'Supports': { return clinicalSignificance.toLowerCase(); }
                     }
                 }
                 case 'Adverse Response':
+
                 case 'Reduced Sensitivity':
 
                 case 'Resistance': {
@@ -133,6 +135,7 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                 case 'Sensitivity/Response': {
                     switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }
+
                         case 'Supports': { return 'sensitivity'; }
                     }
                 }

From a4f0aad567c7b669124733909624312bc05596f1 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 14:37:08 -0700
Subject: [PATCH 09/23] missing blank line

---
 src/civic/index.js | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/civic/index.js b/src/civic/index.js
index 4fde141f..4ce2fa7d 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -132,6 +132,7 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                 case 'Resistance': {
                     return clinicalSignificance.toLowerCase();
                 }
+
                 case 'Sensitivity/Response': {
                     switch (evidenceDirection) { // eslint-disable-line default-case
                         case 'Does Not Support': { return 'no response'; }

From 5c1d291a8c81bde330f5d84134c117989b62eede Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 20 May 2021 15:13:50 -0700
Subject: [PATCH 10/23] fixing title case for Does Not Support

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

diff --git a/test/civic.test.js b/test/civic.test.js
index 9912a894..1d5d59ba 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -635,8 +635,8 @@ describe('translateRelevance', () => {
         ['Predisposing', 'Supports', 'Pathogenic', 'pathogenic'],
         ['Predisposing', 'Supports', 'Likely Pathogenic', 'likely pathogenic'],
         ['Functional', 'Supports', 'Gain of Function', 'gain of function'],
-        ['Predictive', 'Does not Support', 'Sensitivity', 'no response'],
-        ['Predictive', 'Does not Support', 'Sensitivity/Response', 'no response'],
+        ['Predictive', 'Does Not Support', 'Sensitivity', 'no response'],
+        ['Predictive', 'Does Not Support', 'Sensitivity/Response', 'no response'],
     ])(
         '%s|%s|%s returns %s', (evidenceType, evidenceDirection, clinicalSignificance, expected) => {
             expect(translateRelevance(evidenceType, evidenceDirection, clinicalSignificance)).toEqual(expected);

From 798b077848649b7d1b5b389c1668794d264ace59 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Tue, 25 May 2021 14:23:37 -0700
Subject: [PATCH 11/23] add fusion exon example

---
 test/civic.test.js | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/test/civic.test.js b/test/civic.test.js
index 1d5d59ba..e9883995 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -258,6 +258,25 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
+    test('fusion with new exon position notation', () => {
+        // EML4-ALK e20-e20
+        // ALK FUSIONS
+        const variants = normalizeVariantRecord({
+            entrezId: 1,
+            entrezName: 'ALK',
+            name: 'EML4-ALK e20-e20',
+        });
+        expect(variants).toEqual([
+            {
+                positional: true,
+                reference1: { name: 'eml4' },
+                reference2: { name: 'alk', sourceId: '1' },
+                variant: 'fusion(e.20,e.20)',
+            },
+        ]);
+    });
+
+
     test('fusion with reference2 input gene', () => {
         // EML4-ALK E20;A20
         // ALK FUSIONS

From cb4e0aab758fa7c028bb03f183db9dbbfa492d8b Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Tue, 25 May 2021 15:25:59 -0700
Subject: [PATCH 12/23] reverting fusion exon example

---
 test/civic.test.js | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/test/civic.test.js b/test/civic.test.js
index e9883995..1d5d59ba 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -258,25 +258,6 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
-    test('fusion with new exon position notation', () => {
-        // EML4-ALK e20-e20
-        // ALK FUSIONS
-        const variants = normalizeVariantRecord({
-            entrezId: 1,
-            entrezName: 'ALK',
-            name: 'EML4-ALK e20-e20',
-        });
-        expect(variants).toEqual([
-            {
-                positional: true,
-                reference1: { name: 'eml4' },
-                reference2: { name: 'alk', sourceId: '1' },
-                variant: 'fusion(e.20,e.20)',
-            },
-        ]);
-    });
-
-
     test('fusion with reference2 input gene', () => {
         // EML4-ALK E20;A20
         // ALK FUSIONS

From 88ddf828481a17779cfc0841163e40eaff525337 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Fri, 28 May 2021 13:51:16 -0700
Subject: [PATCH 13/23] comment out skipping Does Not Support

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

diff --git a/src/civic/index.js b/src/civic/index.js
index 4ce2fa7d..b3c2d17d 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -588,7 +588,7 @@ const downloadEvidenceRecords = async (baseUrl) => {
 
         if (
             record.clinical_significance === 'N/A'
-            || record.evidence_direction === 'Does Not Support'
+//            || record.evidence_direction === 'Does Not Support'
             || (record.clinical_significance === null && record.evidence_type === 'Predictive')
         ) {
             counts.skip++;

From 808f7a8bf19eab695b53b8a7ce7a2114641db4cd Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Fri, 28 May 2021 13:57:28 -0700
Subject: [PATCH 14/23] fixing eslint error

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

diff --git a/src/civic/index.js b/src/civic/index.js
index b3c2d17d..b8fe6072 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -588,7 +588,7 @@ const downloadEvidenceRecords = async (baseUrl) => {
 
         if (
             record.clinical_significance === 'N/A'
-//            || record.evidence_direction === 'Does Not Support'
+            //|| record.evidence_direction === 'Does Not Support'
             || (record.clinical_significance === null && record.evidence_type === 'Predictive')
         ) {
             counts.skip++;

From 27ecdbdaa2f95f27ae43a3efe48e6d68247ffc4e Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Fri, 28 May 2021 14:12:07 -0700
Subject: [PATCH 15/23] fixing eslint error space

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

diff --git a/src/civic/index.js b/src/civic/index.js
index b8fe6072..3cfda653 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -588,7 +588,7 @@ const downloadEvidenceRecords = async (baseUrl) => {
 
         if (
             record.clinical_significance === 'N/A'
-            //|| record.evidence_direction === 'Does Not Support'
+            // || record.evidence_direction === 'Does Not Support'
             || (record.clinical_significance === null && record.evidence_type === 'Predictive')
         ) {
             counts.skip++;

From b202acb3bbb81ad31a8ac323d148d7fd32c7fc38 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Wed, 2 Jun 2021 17:31:42 -0700
Subject: [PATCH 16/23] modify order of if/switch blocks for Predictive

---
 src/civic/index.js | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 3cfda653..3395ac81 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -117,31 +117,32 @@ const validateEvidenceSpec = ajv.compile({
 const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificance) => {
     switch (evidenceType) { // eslint-disable-line default-case
         case 'Predictive': {
-            switch (clinicalSignificance) { // eslint-disable-line default-case
-                case 'Sensitivity': {
-                    switch (evidenceDirection) { // eslint-disable-line default-case
-                        case 'Does Not Support': { return 'no response'; }
+            if (evidenceDirection == 'Does Not Support') {
+                switch (clinicalSignificance) { // eslint-disable-line default-case
+                    case 'Sensitivity':
 
-                        case 'Supports': { return clinicalSignificance.toLowerCase(); }
+                    case 'Sensitivity/Response': {
+                        return 'no response';
                     }
                 }
-                case 'Adverse Response':
-
-                case 'Reduced Sensitivity':
-
-                case 'Resistance': {
-                    return clinicalSignificance.toLowerCase();
-                }
 
-                case 'Sensitivity/Response': {
-                    switch (evidenceDirection) { // eslint-disable-line default-case
-                        case 'Does Not Support': { return 'no response'; }
+            } else if (evidenceDirection == 'Supports') {
+                switch (clinicalSignificance) { // eslint-disable-line default-case
+                    case 'Sensitivity':
+                    case 'Adverse Response':
+                    case 'Reduced Sensitivity':
 
-                        case 'Supports': { return 'sensitivity'; }
+                    case 'Resistance': {
+                        return clinicalSignificance.toLowerCase();
                     }
+
+                    case 'Sensitivity/Response': { return 'sensitivity'; }
                 }
             }
-            break;
+
+            throw new Error(
+                `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
+            );
         }
 
         case 'Functional': {
@@ -588,7 +589,6 @@ const downloadEvidenceRecords = async (baseUrl) => {
 
         if (
             record.clinical_significance === 'N/A'
-            // || record.evidence_direction === 'Does Not Support'
             || (record.clinical_significance === null && record.evidence_type === 'Predictive')
         ) {
             counts.skip++;

From bbfa2a5641aaecccf864aa0b31bdf7b49baba01b Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Wed, 2 Jun 2021 17:37:31 -0700
Subject: [PATCH 17/23] fixing eslint errors line 120 and 129

---
 src/civic/index.js | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index 3395ac81..adae8712 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -117,7 +117,7 @@ const validateEvidenceSpec = ajv.compile({
 const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificance) => {
     switch (evidenceType) { // eslint-disable-line default-case
         case 'Predictive': {
-            if (evidenceDirection == 'Does Not Support') {
+            if (evidenceDirection === 'Does Not Support') {
                 switch (clinicalSignificance) { // eslint-disable-line default-case
                     case 'Sensitivity':
 
@@ -125,8 +125,7 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                         return 'no response';
                     }
                 }
-
-            } else if (evidenceDirection == 'Supports') {
+            } else if (evidenceDirection === 'Supports') {
                 switch (clinicalSignificance) { // eslint-disable-line default-case
                     case 'Sensitivity':
                     case 'Adverse Response':

From bd747e7f9429c341db13c6912aa5b64e395aac61 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Thu, 3 Jun 2021 14:59:59 -0700
Subject: [PATCH 18/23] replace throw error with a break

---
 src/civic/index.js | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/src/civic/index.js b/src/civic/index.js
index adae8712..4882e6e3 100644
--- a/src/civic/index.js
+++ b/src/civic/index.js
@@ -138,10 +138,7 @@ const translateRelevance = (evidenceType, evidenceDirection, clinicalSignificanc
                     case 'Sensitivity/Response': { return 'sensitivity'; }
                 }
             }
-
-            throw new Error(
-                `unable to process relevance (${JSON.stringify({ clinicalSignificance, evidenceDirection, evidenceType })})`,
-            );
+            break;
         }
 
         case 'Functional': {

From 533210f46439329610ad5e32e9d896af4fbb8980 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Mon, 7 Jun 2021 11:16:05 -0700
Subject: [PATCH 19/23] add test for new civic exon notation and modify regex

---
 src/civic/variant.js |  2 +-
 test/civic.test.js   | 18 ++++++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/src/civic/variant.js b/src/civic/variant.js
index df131f3e..5117010e 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -185,7 +185,7 @@ const normalizeVariantRecord = ({
         let rest = { type: 'fusion' };
 
         if (tail) {
-            if (match = /^[a-z](\d+);[a-z](\d+)$/.exec(tail || '')) {
+            if (match = /^[e](\d+)-[e](\d+)$/.exec(tail || '')) {
                 const [, exon1, exon2] = match;
                 rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
             } else {
diff --git a/test/civic.test.js b/test/civic.test.js
index 1d5d59ba..e276bc62 100644
--- a/test/civic.test.js
+++ b/test/civic.test.js
@@ -258,6 +258,24 @@ describe('normalizeVariantRecord', () => {
         ]);
     });
 
+    test('fusion with new exon notation', () => {
+        // EWSR1-FLI1 e7-e6
+        // FLI1 Fusion
+        const variants = normalizeVariantRecord({
+            entrezId: 1,
+            entrezName: 'FLI1',
+            name: 'EWSR1-FLI1 e7-e6',
+        });
+        expect(variants).toEqual([
+            {
+                positional: true,
+                reference1: { name: 'ewsr1' },
+                reference2: { name: 'fli1', sourceId: '1' },
+                variant: 'fusion(e.7,e.6)',
+            },
+        ]);
+    });
+
     test('fusion with reference2 input gene', () => {
         // EML4-ALK E20;A20
         // ALK FUSIONS

From 53397b47d3685f3c18efe132addbfd5e40a577f3 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Mon, 7 Jun 2021 12:10:42 -0700
Subject: [PATCH 20/23] adding lines to load old fusion exon notation

---
 src/civic/variant.js | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/civic/variant.js b/src/civic/variant.js
index 5117010e..bf8311ee 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -188,6 +188,9 @@ const normalizeVariantRecord = ({
             if (match = /^[e](\d+)-[e](\d+)$/.exec(tail || '')) {
                 const [, exon1, exon2] = match;
                 rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
+            } else if (match = /^[a-z](\d+);[a-z](\d+)$/.exec(tail || '')) {
+                const [, exon1, exon2] = match;
+                rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
             } else {
                 return [
                     ...normalizeVariantRecord({ entrezId, entrezName, name: `${gene1}-${gene2}` }),

From 42e54677ce794e7b4345a53dcddf6870c2d5c431 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Mon, 7 Jun 2021 14:04:21 -0700
Subject: [PATCH 21/23] removing square brackets

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

diff --git a/src/civic/variant.js b/src/civic/variant.js
index bf8311ee..e92b16a5 100644
--- a/src/civic/variant.js
+++ b/src/civic/variant.js
@@ -185,7 +185,7 @@ const normalizeVariantRecord = ({
         let rest = { type: 'fusion' };
 
         if (tail) {
-            if (match = /^[e](\d+)-[e](\d+)$/.exec(tail || '')) {
+            if (match = /^e(\d+)-e(\d+)$/.exec(tail || '')) {
                 const [, exon1, exon2] = match;
                 rest = { positional: true, variant: `fusion(e.${exon1},e.${exon2})` };
             } else if (match = /^[a-z](\d+);[a-z](\d+)$/.exec(tail || '')) {

From 114a914ba3f90756f490dc4c6350513de412747e Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Wed, 23 Jun 2021 13:31:04 -0700
Subject: [PATCH 22/23] update version

---
 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 75073f36..e0516605 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
-  "version": "5.1.0",
+  "version": "5.1.1",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/package.json b/package.json
index 4c7fda72..1519f315 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
   "main": "src/index.js",
-  "version": "5.1.0",
+  "version": "5.1.1",
   "repository": {
     "type": "git",
     "url": "https://github.com/bcgsc/pori_graphkb_loader.git"

From b7887520568af0c7349dedc973d5466cbf6b8362 Mon Sep 17 00:00:00 2001
From: Cam Grisdale <cgrisdale@bcgsc.ca>
Date: Mon, 5 Jul 2021 13:25:17 -0700
Subject: [PATCH 23/23] changing release version to 5.2.0

---
 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 e0516605..32e336e1 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,6 +1,6 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
-  "version": "5.1.1",
+  "version": "5.2.0",
   "lockfileVersion": 1,
   "requires": true,
   "dependencies": {
diff --git a/package.json b/package.json
index 1519f315..ca6c74f6 100644
--- a/package.json
+++ b/package.json
@@ -1,7 +1,7 @@
 {
   "name": "@bcgsc-pori/graphkb-loader",
   "main": "src/index.js",
-  "version": "5.1.1",
+  "version": "5.2.0",
   "repository": {
     "type": "git",
     "url": "https://github.com/bcgsc/pori_graphkb_loader.git"