Merge pull request #15 from bcgsc/master

Master back to dev

.eslintrc.json

@@ -34,7 +34,16 @@
             "unix"
         ],
         "max-classes-per-file": "off",
-        "max-len": "warn",
+        "max-len": [
+            "warn",
+            {
+                "code": 100,
+                "ignoreComments": true,
+                "ignoreStrings": true,
+                "ignoreTemplateLiterals": true,
+                "ignoreTrailingComments": true
+            }
+        ],
         "multiline-ternary": [
             "error",
             "always"

.github/workflows/npm-test.yml

@@ -16,6 +16,9 @@ jobs:
           node-version: ${{ matrix.node }}
       - run: npm ci
       - run: npm audit --production
+      - run: npm run lint
+      - name: test build
+        run: npm run build
       - run: npm test
       - name: Publish Unit Test Results
         uses: EnricoMi/[email protected]

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bcgsc-pori/graphkb-parser",
-  "version": "1.1.3",
+  "version": "2.0.0",
   "description": "A package for parsing and recreating HGVS-like variant notation used in GraphKB",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -11,6 +11,7 @@
     "test": "NODE_ENV=test jest --config config/jest.config.js --detectOpenHandles --forceExit",
     "build": "tsc",
     "clean": "rm -rf dist",
+    "prepublishOnly": "npm ci && npm run build",
     "lint": "eslint src test -c .eslintrc.json"
   },
   "repository": {

src/constants.ts

@@ -81,10 +81,10 @@ const TYPES_TO_NOTATION: Readonly<{ [key: string]: string }> = addTypeMappings()
 
 type Prefix = 'g' | 'y' | 'i' | 'c' | 'r' | 'e' | 'n' | 'p';
 /**
- * the mapping of positional variant notation prefixes to their corresponging position classes
+ * the mapping of positional variant notation prefixes to their corresponding position classes
  * @namespace
  *
- * @property {string} g genomic postions
+ * @property {string} g genomic positions
  * @property {string} i intronic positions
  * @property {string} e exonic positions
  * @property {string} p protein positions (amino acid coordinates)

src/continuous.ts

@@ -73,16 +73,23 @@ const convert3to1 = (notation: string): string => {
  * Extract and return the position range
  * @param {string} string
  */
-const extractPositions = (prefix: Prefix, string: string): { input: string; start?: AnyPosition; end?: AnyPosition } => {
+const extractPositions = (
+    prefix: Prefix,
+    string: string,
+): { input: string; start?: AnyPosition; end?: AnyPosition } => {
     let input: string;
 
     if (string.startsWith('(')) {
         // expect the first breakpoint to be a range of two positions
         if (string.indexOf(')') < 0) {
-            throw new ParsingError('Expected a range of positions. Missing the closing parenthesis');
+            throw new ParsingError(
+                'Expected a range of positions. Missing the closing parenthesis',
+            );
         }
         if (string.indexOf('_') < 0) {
-            throw new ParsingError('Positions within a range must be separated by an underscore. Missing underscore');
+            throw new ParsingError(
+                'Positions within a range must be separated by an underscore. Missing underscore',
+            );
         }
         input = string.slice(0, string.indexOf(')') + 1);
         return {
@@ -242,7 +249,7 @@ const parseContinuous = (inputString) => {
 
             if (alt === '*' && truncation !== 1) {
                 throw new ParsingError({
-                    message: 'invalid framshift specifies a non-immeadiate truncation which conflicts with the terminating alt seqeuence',
+                    message: 'invalid frameshift specifies a non-immediate truncation which conflicts with the terminating alt sequence',
                     violatedAttr: 'truncation',
                 });
             }
@@ -279,7 +286,7 @@ const parseContinuous = (inputString) => {
             });
         }
     }
-    // check for innapropriate types
+    // check for inappropriate types
     if (prefix === 'y') {
         if (refSeq) {
             throw new ParsingError({
@@ -323,7 +330,12 @@ const parseContinuous = (inputString) => {
             refSeq = break1Start.longRefAA || break1Start.refAA;
         }
         // covert to 1AA code? check if any of the positions were converted
-        const convert = [break1Start, break1End, break2Start, break2End].some((x) => x && x.longRefAA);
+        const convert = [
+            break1Start,
+            break1End,
+            break2Start,
+            break2End,
+        ].some((x) => x && x.longRefAA);
 
         if (convert) {
             if (untemplatedSeq) {

src/error.ts

@@ -5,7 +5,7 @@ import jc from 'json-cycle';
  * @property {string} message the error message
  * @property {string} name the error name (generally the same as the error class)
  * @property {string} stack the stack trace associated with this error
- * @property {Object} content additional properties assigined to the error to aid in debugging
+ * @property {Object} content additional properties assigned to the error to aid in debugging
  */
 class ErrorMixin extends Error {
     message: string;
@@ -40,7 +40,7 @@ class ErrorMixin extends Error {
     }
 
     /**
-     * @return {Object} the JSON respresenation of this error
+     * @return {Object} the JSON representation of this error
      */
     toJSON() {
         return jc.decycle(Object.assign(this.content, {

src/position.ts

@@ -97,7 +97,7 @@ const createCytoBandPosition = ({ arm, majorBand, minorBand }): CytobandPosition
     return result;
 };
 
-const checkBasicPosition = (pos: any, allowNegative = false): number | null => {
+const checkBasicPosition = (pos: unknown, allowNegative = false): number | null => {
     if (pos === '?' || pos === null) {
         return null;
     }
@@ -110,7 +110,11 @@ const checkBasicPosition = (pos: any, allowNegative = false): number | null => {
     return Number(pos);
 };
 
-const createBasicPosition = (pos: any, prefix: Prefix, allowNegative = false): BasicPosition => {
+const createBasicPosition = (
+    pos: unknown,
+    prefix: Prefix,
+    allowNegative = false,
+): BasicPosition => {
     const result = {
         [CLASS_FIELD]: PREFIX_CLASS[prefix],
         pos: checkBasicPosition(pos, allowNegative),
@@ -120,7 +124,9 @@ const createBasicPosition = (pos: any, prefix: Prefix, allowNegative = false): B
 };
 
 const createCdsLikePosition = ({ offset, pos }, prefix: 'c' | 'n' | 'r'): CdsLikePosition => {
-    const result: any = { ...createBasicPosition(pos, prefix, true) };
+    const result: CdsLikePosition = {
+        ...createBasicPosition(pos, prefix, true) as CdsLikePosition,
+    };
 
     if (offset !== undefined) {
         result.offset = Number(offset);
@@ -135,9 +141,13 @@ const createCdsLikePosition = ({ offset, pos }, prefix: 'c' | 'n' | 'r'): CdsLik
     return result;
 };
 
-const createProteinPosition = ({ refAA, pos }: { refAA: string; pos: string | number | null }): ProteinPosition => {
-    const prefix = 'p';
-    const result: any = { ...createBasicPosition(pos, prefix), longRefAA: null, refAA };
+const createProteinPosition = ({
+    refAA,
+    pos,
+}: { refAA: string; pos: string | number | null }): ProteinPosition => {
+    const result: ProteinPosition = {
+        ...createBasicPosition(pos, 'p') as ProteinPosition, longRefAA: null, refAA,
+    };
 
     if (result.refAA) {
         if (result.refAA === '?') {
@@ -214,7 +224,11 @@ const convertPositionToString = (position) => {
  *
  * @returns the string representation of a breakpoint or breakpoint range including the prefix
  */
-const createBreakRepr = (start: AnyPosition, end: AnyPosition | null = null, multiFeature = false): string => {
+const createBreakRepr = (
+    start: AnyPosition,
+    end: AnyPosition | null = null,
+    multiFeature = false,
+): string => {
     if (end) {
         if (start.prefix !== end.prefix) {
             throw new ParsingError('Mismatch prefix in range');