@metrichor/epi2me-api - npm Package Compare versions

Comparing version 6.0.7479716 to 6.0.7581324

cjs/src/epi2me-fs.d.ts

@@ -23,2 +23,5 @@ /// <reference types="node" />
     static GraphQL: typeof GraphQLFS;
+    /**
+     * @deprecated use `getExperiments` instead
+     */
     SampleReader: SampleReader;
@@ -25,0 +28,0 @@ telemetryLogStream?: fs.WriteStream;

cjs/src/epi2me-fs.js

@@ -77,2 +77,5 @@ /**
     constructor(opts) {
+        /**
+         * @deprecated use `getExperiments` instead
+         */
         this.SampleReader = new sampleReader.SampleReader();
@@ -214,3 +217,3 @@ this.stopped = true;
     async stopAnalysis() {
-        // If we stop the cloud, there's no point uploading anymore
+        // If we stop the cloud, there's no point uploading any more
         this.stopUpload();
@@ -242,3 +245,3 @@ // This will stop all the intervals on their next call
         const credentials$1 = new credentials.Epi2meCredentials(this.fetchToken, this.config.options.sessionGrace);
-        // Will need to prefetch a token to acccess region before creating the S3 service
+        // Will need to prefetch a token to access region before creating the S3 service
         return new AWS__namespace.S3(Object.assign(Object.assign({ useAccelerateEndpoint: this.config.options.awsAcceleration === 'on' }, options), { region: this.config.instance.region, credentials: credentials$1, httpOptions: {
@@ -685,3 +688,3 @@ agent: this.proxyAgent,
             catch (err) {
-                this.log.error(NodeError.NestedError.formatMessage('error writing telemtry', err));
+                this.log.error(NodeError.NestedError.formatMessage('error writing telemetry', err));
             }
@@ -698,3 +701,3 @@ if (this.config.options.telemetryCb) {
         const idWorkflowInstance = this.config.instance.id_workflow_instance;
-        let folder = path__default["default"].join(tsRuntimeTypecheck.asString(this.config.options.outputFolder), tsRuntimeTypecheck.isUndefined(idWorkflowInstance) ? '' : tsRuntimeTypecheck.makeString(idWorkflowInstance));
+        let folder = path__default["default"].join(tsRuntimeTypecheck.asString(this.config.options.outputFolder), `${idWorkflowInstance !== null && idWorkflowInstance !== void 0 ? idWorkflowInstance : ''}`);
         const telemetryHintsFolder = tsRuntimeTypecheck.asOptString((_a = tsRuntimeTypecheck.asOptDictionary(telemetry === null || telemetry === void 0 ? void 0 : telemetry.hints)) === null || _a === void 0 ? void 0 : _a.folder);
@@ -710,3 +713,3 @@ /* MC-940: use folder hinting if present */
                 .map((o) => o.toUpperCase()); // MC-5612 cross-platform uppercase "pass" folder
-            folder = path__default["default"].join.apply(null, [folder, ...codes]);
+            folder = path__default["default"].join(...[folder, ...codes]);
         }
@@ -713,0 +716,0 @@ try {

cjs/src/factory.d.ts

@@ -25,2 +25,5 @@ /// <reference types="node" />
     get graphQL(): GraphQLFS;
+    /**
+     * @deprecated use `getExperiments` instead
+     */
     get sampleReader(): SampleReader;
@@ -27,0 +30,0 @@ get proxyAgent(): Agent | undefined;

cjs/src/factory.js

@@ -51,2 +51,5 @@ /**
     }
+    /**
+     * @deprecated use `getExperiments` instead
+     */
     get sampleReader() {
@@ -53,0 +56,0 @@ return this.primary.SampleReader;

cjs/src/filestats/default.d.ts

@@ -1,4 +0,2 @@
-export declare function genericFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-}>;
+import type { DefaultStats } from './filestats.type';
+export declare function genericFileStatistics(filePath: string): Promise<DefaultStats>;

cjs/src/filestats/default.js

@@ -16,5 +16,4 @@ /**
 async function genericFileStatistics(filePath) {
-    return fs__default["default"].promises.stat(filePath).then((d) => {
-        return { type: 'bytes', bytes: d.size };
-    });
+    const { size: bytes } = await fs__default["default"].promises.stat(filePath);
+    return { type: 'bytes', bytes };
 }
@@ -21,0 +20,0 @@

cjs/src/filestats/fasta.d.ts

@@ -1,5 +0,2 @@
-export declare function fastaFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    sequences: number;
-}>;
+import type { FastaStats } from './filestats.type';
+export declare function fastaFileStatistics(filePath: string): Promise<FastaStats>;

cjs/src/filestats/fasta.js

@@ -19,3 +19,2 @@ /**
     let lineCount = 1;
-    let idx = -1;
     if (stat.size === 0) {
@@ -29,3 +28,3 @@ return {
     const readStream = fs__default["default"].createReadStream(filePath).on('data', (buffer) => {
-        idx = -1;
+        let idx = -1;
         lineCount -= 1;
@@ -32,0 +31,0 @@ do {

cjs/src/filestats/fastq.d.ts

@@ -1,5 +0,2 @@
-export declare function fastqFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    reads: number;
-}>;
+import type { FastqStats } from './filestats.type';
+export declare function fastqFileStatistics(filePath: string): Promise<FastqStats>;

cjs/src/filestats/fastq.js

@@ -15,31 +15,27 @@ /**
 
-function fastqFileStatistics(filePath) {
+const LINES_PER_READ = 4;
+async function fastqFileStatistics(filePath) {
+    let lineCount = 1;
+    const stat = await fs__default["default"].promises.stat(filePath);
+    if (stat.size === 0) {
+        return {
+            type: 'fastq',
+            bytes: 0,
+            reads: 0,
+        };
+    }
+    const readStream = fs__default["default"].createReadStream(filePath).on('data', (buffer) => {
+        let idx = -1;
+        lineCount -= 1;
+        do {
+            idx = buffer.indexOf(10, idx + 1);
+            lineCount += 1;
+        } while (idx !== -1);
+    });
     return new Promise((resolve, reject) => {
-        const linesPerRead = 4;
-        let lineCount = 1;
-        let idx = -1;
-        let stat = {
-            size: 0,
-        };
-        try {
-            // TODO make this async
-            stat = fs__default["default"].statSync(filePath);
-        }
-        catch (e) {
-            reject(e);
-            return;
-        }
-        fs__default["default"].createReadStream(filePath)
-            .on('data', (buffer) => {
-            idx = -1;
-            lineCount -= 1;
-            do {
-                idx = buffer.indexOf(10, idx + 1);
-                lineCount += 1;
-            } while (idx !== -1);
-        })
+        readStream
             .on('end', () => resolve({
             type: 'fastq',
             bytes: stat.size,
-            reads: Math.floor(lineCount / linesPerRead),
+            reads: Math.floor(lineCount / LINES_PER_READ),
         }))
@@ -46,0 +42,0 @@ .on('error', reject);

cjs/src/filestats/fastqgz.d.ts

@@ -1,5 +0,2 @@
-export declare function fastqgzFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    reads: number;
-}>;
+import type { FastqGZStats } from './filestats.type';
+export declare function fastqgzFileStatistics(filePath: string): Promise<FastqGZStats>;

cjs/src/filestats/fastqgz.js

@@ -27,3 +27,2 @@ /**
     let lineCount = 1;
-    let idx = -1;
     const gunzipStream = fs__default["default"]
@@ -33,3 +32,3 @@ .createReadStream(filePath)
         .on('data', (buffer) => {
-        idx = -1;
+        let idx = -1;
         lineCount -= 1;
@@ -36,0 +35,0 @@ do {

cjs/src/filestats/filestats.type.d.ts

@@ -0,1 +1,20 @@
+export interface FastqStats {
+    type: 'fastq';
+    bytes: number;
+    reads: number;
+}
+export interface FastaStats {
+    type: 'fasta';
+    bytes: number;
+    sequences: number;
+}
+export interface FastqGZStats {
+    type: 'gz';
+    bytes: number;
+    reads: number;
+}
+export interface DefaultStats {
+    type: 'bytes';
+    bytes: number;
+}
 export interface MappedFileStats {
@@ -2,0 +21,0 @@ type: string;

mjs/src/epi2me-fs.d.ts

@@ -23,2 +23,5 @@ /// <reference types="node" />
     static GraphQL: typeof GraphQLFS;
+    /**
+     * @deprecated use `getExperiments` instead
+     */
     SampleReader: SampleReader;
@@ -25,0 +28,0 @@ telemetryLogStream?: fs.WriteStream;

mjs/src/factory.d.ts

@@ -25,2 +25,5 @@ /// <reference types="node" />
     get graphQL(): GraphQLFS;
+    /**
+     * @deprecated use `getExperiments` instead
+     */
     get sampleReader(): SampleReader;
@@ -27,0 +30,0 @@ get proxyAgent(): Agent | undefined;

mjs/src/filestats/default.d.ts

@@ -1,4 +0,2 @@
-export declare function genericFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-}>;
+import type { DefaultStats } from './filestats.type';
+export declare function genericFileStatistics(filePath: string): Promise<DefaultStats>;

mjs/src/filestats/fasta.d.ts

@@ -1,5 +0,2 @@
-export declare function fastaFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    sequences: number;
-}>;
+import type { FastaStats } from './filestats.type';
+export declare function fastaFileStatistics(filePath: string): Promise<FastaStats>;

mjs/src/filestats/fastq.d.ts

@@ -1,5 +0,2 @@
-export declare function fastqFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    reads: number;
-}>;
+import type { FastqStats } from './filestats.type';
+export declare function fastqFileStatistics(filePath: string): Promise<FastqStats>;

mjs/src/filestats/fastqgz.d.ts

@@ -1,5 +0,2 @@
-export declare function fastqgzFileStatistics(filePath: string): Promise<{
-    type: string;
-    bytes: number;
-    reads: number;
-}>;
+import type { FastqGZStats } from './filestats.type';
+export declare function fastqgzFileStatistics(filePath: string): Promise<FastqGZStats>;

mjs/src/filestats/filestats.type.d.ts

@@ -0,1 +1,20 @@
+export interface FastqStats {
+    type: 'fastq';
+    bytes: number;
+    reads: number;
+}
+export interface FastaStats {
+    type: 'fasta';
+    bytes: number;
+    sequences: number;
+}
+export interface FastqGZStats {
+    type: 'gz';
+    bytes: number;
+    reads: number;
+}
+export interface DefaultStats {
+    type: 'bytes';
+    bytes: number;
+}
 export interface MappedFileStats {
@@ -2,0 +21,0 @@ type: string;

package.json

 {
   "name": "@metrichor/epi2me-api",
-  "version": "6.0.7479716",
+  "version": "6.0.7581324",
   "license": "MPL-2.0",
@@ -17,5 +17,2 @@ "repository": "[e-mail]:nanoporetech/epi2me-api.git",
     "@apollo/client": "^3.4.16",
-    "@grpc/grpc-js": "^1.3.7",
-    "@improbable-eng/grpc-web": "^0.14.1",
-    "@improbable-eng/grpc-web-node-http-transport": "^0.14.1",
     "@types/socket.io-client": "^3.0.0",
@@ -27,3 +24,2 @@ "aws-sdk": "^2.1002.0",
     "fs-inspect": "^1.0.3",
-    "google-protobuf": "^3.18.1",
     "graphql": "^15.6.1",
@@ -30,0 +26,0 @@ "graphql-tag": "^2.12.5",

New alerts

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License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

582218

increased by0.16%

Dependency count

14

decreased by-22.22%

Lines of code

12155

increased by0.21%

Dependency changes

• - Removed@grpc/grpc-js@^1.3.7

• - Removed@improbable-eng/grpc-web@^0.14.1

• - Removed@improbable-eng/grpc-web-node-http-transport@^0.14.1

• - Removedgoogle-protobuf@^3.18.1

• - Removed@grpc/grpc-js@1.12.5(transitive)

• - Removed@grpc/proto-loader@0.7.13(transitive)

• - Removed@improbable-eng/grpc-web@0.14.1(transitive)

• - Removed@improbable-eng/grpc-web-node-http-transport@0.14.1(transitive)

• - Removed@js-sdsl/ordered-map@4.4.2(transitive)

• - Removed@protobufjs/aspromise@1.1.2(transitive)

• - Removed@protobufjs/base64@1.1.2(transitive)

• - Removed@protobufjs/codegen@2.0.4(transitive)

• - Removed@protobufjs/eventemitter@1.1.0(transitive)

• - Removed@protobufjs/fetch@1.1.0(transitive)

• - Removed@protobufjs/float@1.0.2(transitive)

• - Removed@protobufjs/inquire@1.1.0(transitive)

• - Removed@protobufjs/path@1.1.2(transitive)

• - Removed@protobufjs/pool@1.1.0(transitive)

• - Removed@protobufjs/utf8@1.1.0(transitive)

• - Removed@types/node@22.10.2(transitive)

• - Removedansi-regex@5.0.1(transitive)

• - Removedansi-styles@4.3.0(transitive)

• - Removedbrowser-headers@0.4.1(transitive)

• - Removedcliui@8.0.1(transitive)

• - Removedcolor-convert@2.0.1(transitive)

• - Removedcolor-name@1.1.4(transitive)

• - Removedemoji-regex@8.0.0(transitive)

• - Removedescalade@3.2.0(transitive)

• - Removedget-caller-file@2.0.5(transitive)

• - Removedgoogle-protobuf@3.21.4(transitive)

• - Removedis-fullwidth-code-point@3.0.0(transitive)

• - Removedlodash.camelcase@4.3.0(transitive)

• - Removedlong@5.2.3(transitive)

• - Removedprotobufjs@7.4.0(transitive)

• - Removedrequire-directory@2.1.1(transitive)

• - Removedstring-width@4.2.3(transitive)

• - Removedstrip-ansi@6.0.1(transitive)

• - Removedundici-types@6.20.0(transitive)

• - Removedwrap-ansi@7.0.0(transitive)

• - Removedy18n@5.0.8(transitive)

• - Removedyargs@17.7.2(transitive)

• - Removedyargs-parser@21.1.1(transitive)